Correlation between copy number variations of arm-level result and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C17D2SMQ
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/C17D2SMQ
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 80 arm-level events and 12 molecular subtypes across 490 patients, 115 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 15q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 17q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 19p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 6p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 9q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 19p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'MRNASEQ_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 115 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
17q gain 156 (32%) 334 0.000922
(0.751) 		2.89e-05
(0.0255) 		1.51e-15
(1.44e-12) 		5.76e-10
(5.41e-07) 		0.234
(1.00) 		0.546
(1.00) 		1.99e-09
(1.86e-06) 		3.7e-10
(3.49e-07) 		3.5e-05
(0.0308) 		0.00236
(1.00) 		2.38e-07
(0.00022) 		5.09e-06
(0.00459)
1p loss 147 (30%) 343 1.56e-05
(0.0139) 		1.84e-06
(0.00168) 		1.17e-20
(1.12e-17) 		2.16e-10
(2.04e-07) 		0.882
(1.00) 		0.086
(1.00) 		1.56e-12
(1.48e-09) 		2.66e-13
(2.54e-10) 		0.000193
(0.165) 		6.55e-05
(0.0573) 		0.0103
(1.00) 		0.00035
(0.295)
9q loss 239 (49%) 251 1.14e-05
(0.0102) 		7.37e-06
(0.00661) 		1.19e-17
(1.14e-14) 		1.75e-09
(1.64e-06) 		0.167
(1.00) 		0.0178
(1.00) 		5.61e-20
(5.38e-17) 		5.03e-18
(4.82e-15) 		2.32e-08
(2.16e-05) 		3.77e-10
(3.55e-07) 		0.000647
(0.532) 		0.00285
(1.00)
4p loss 307 (63%) 183 0.000795
(0.651) 		0.00551
(1.00) 		6.51e-13
(6.2e-10) 		8.23e-08
(7.63e-05) 		0.207
(1.00) 		0.122
(1.00) 		1.74e-06
(0.00158) 		3.08e-06
(0.00279) 		0.000121
(0.104) 		0.46
(1.00) 		0.000114
(0.0983) 		1.23e-05
(0.011)
10p loss 210 (43%) 280 0.204
(1.00) 		0.289
(1.00) 		3.79e-06
(0.00342) 		2.74e-08
(2.54e-05) 		0.467
(1.00) 		0.284
(1.00) 		1.35e-06
(0.00123) 		4.7e-08
(4.36e-05) 		6.47e-05
(0.0567) 		1.37e-05
(0.0122) 		0.000586
(0.486) 		0.0134
(1.00)
10q loss 223 (46%) 267 0.00133
(1.00) 		0.000824
(0.673) 		1.61e-06
(0.00146) 		3.67e-07
(0.000338) 		0.0953
(1.00) 		0.0927
(1.00) 		6.67e-09
(6.22e-06) 		7.16e-10
(6.71e-07) 		0.000171
(0.146) 		8.34e-06
(0.00748) 		0.000548
(0.456) 		0.026
(1.00)
7q gain 214 (44%) 276 0.00138
(1.00) 		0.00392
(1.00) 		2.64e-11
(2.5e-08) 		3.22e-07
(0.000297) 		0.97
(1.00) 		0.302
(1.00) 		4.4e-09
(4.11e-06) 		7.38e-10
(6.92e-07) 		0.000777
(0.637) 		0.000128
(0.11) 		0.00454
(1.00) 		0.00108
(0.878)
9q gain 91 (19%) 399 0.0157
(1.00) 		0.0323
(1.00) 		2.89e-12
(2.75e-09) 		2.57e-10
(2.42e-07) 		0.0584
(1.00) 		0.0133
(1.00) 		4.94e-14
(4.71e-11) 		6.48e-16
(6.19e-13) 		4.34e-05
(0.0382) 		0.00118
(0.948) 		0.00135
(1.00) 		0.00108
(0.875)
14q loss 165 (34%) 325 7.22e-05
(0.0631) 		0.0408
(1.00) 		0.0598
(1.00) 		0.113
(1.00) 		0.0524
(1.00) 		0.185
(1.00) 		3.92e-10
(3.69e-07) 		2.64e-12
(2.51e-09) 		1.67e-07
(0.000155) 		3.77e-06
(0.00341) 		0.0103
(1.00) 		0.0144
(1.00)
2p gain 218 (44%) 272 0.0781
(1.00) 		0.0433
(1.00) 		1.09e-11
(1.03e-08) 		4.28e-06
(0.00386) 		0.403
(1.00) 		0.484
(1.00) 		1.27e-06
(0.00116) 		3.22e-05
(0.0285) 		0.00113
(0.911) 		0.00215
(1.00) 		0.000609
(0.503) 		0.0018
(1.00)
7p gain 234 (48%) 256 0.0364
(1.00) 		0.0354
(1.00) 		1.97e-05
(0.0175) 		0.000158
(0.136) 		0.664
(1.00) 		0.871
(1.00) 		0.000119
(0.103) 		6.01e-07
(0.000552) 		0.00464
(1.00) 		0.00495
(1.00) 		0.00348
(1.00) 		0.0345
(1.00)
9p gain 60 (12%) 430 0.0924
(1.00) 		0.211
(1.00) 		0.000108
(0.0939) 		9.67e-05
(0.084) 		0.186
(1.00) 		0.0262
(1.00) 		7.21e-06
(0.00648) 		9.86e-07
(0.000903) 		0.0839
(1.00) 		0.2
(1.00) 		0.00709
(1.00) 		0.0579
(1.00)
4q loss 290 (59%) 200 0.00123
(0.991) 		0.00409
(1.00) 		5.18e-11
(4.9e-08) 		3.28e-05
(0.029) 		0.255
(1.00) 		0.338
(1.00) 		2.88e-06
(0.00262) 		4.13e-06
(0.00373) 		0.00724
(1.00) 		0.0548
(1.00) 		0.00847
(1.00) 		0.00157
(1.00)
6p loss 109 (22%) 381 0.0365
(1.00) 		0.0103
(1.00) 		0.000254
(0.215) 		9.41e-05
(0.0819) 		0.145
(1.00) 		0.145
(1.00) 		7.11e-06
(0.0064) 		5.58e-07
(0.000513) 		0.295
(1.00) 		0.16
(1.00) 		0.0052
(1.00) 		0.0239
(1.00)
1q gain 199 (41%) 291 0.671
(1.00) 		0.704
(1.00) 		0.000182
(0.156) 		5.66e-05
(0.0497) 		0.571
(1.00) 		0.29
(1.00) 		0.0062
(1.00) 		0.000129
(0.111) 		0.0194
(1.00) 		0.00109
(0.878) 		0.0646
(1.00) 		0.254
(1.00)
17p gain 65 (13%) 425 0.00459
(1.00) 		0.0707
(1.00) 		1.7e-07
(0.000158) 		0.000842
(0.686) 		0.812
(1.00) 		0.268
(1.00) 		0.000128
(0.11) 		4.96e-05
(0.0437) 		0.0203
(1.00) 		0.00314
(1.00) 		0.00427
(1.00) 		0.0234
(1.00)
17q loss 90 (18%) 400 0.00555
(1.00) 		0.00995
(1.00) 		0.000511
(0.427) 		0.00012
(0.103) 		0.335
(1.00) 		0.644
(1.00) 		2.17e-05
(0.0192) 		1.05e-05
(0.00944) 		0.174
(1.00) 		0.0386
(1.00) 		0.0521
(1.00) 		0.000602
(0.498)
xq loss 110 (22%) 380 0.206
(1.00) 		0.238
(1.00) 		0.000279
(0.236) 		0.000573
(0.475) 		0.777
(1.00) 		0.657
(1.00) 		0.0271
(1.00) 		0.0397
(1.00) 		0.000371
(0.311) 		0.108
(1.00) 		8.84e-05
(0.077) 		0.000197
(0.168)
12p gain 224 (46%) 266 0.0187
(1.00) 		0.0906
(1.00) 		5.25e-10
(4.94e-07) 		0.00147
(1.00) 		0.222
(1.00) 		0.63
(1.00) 		6.62e-05
(0.0578) 		0.00415
(1.00) 		0.0235
(1.00) 		0.058
(1.00) 		0.0737
(1.00) 		0.148
(1.00)
18p gain 147 (30%) 343 0.00843
(1.00) 		0.0031
(1.00) 		5.05e-09
(4.72e-06) 		3e-06
(0.00272) 		0.478
(1.00) 		0.221
(1.00) 		0.000828
(0.676) 		0.00212
(1.00) 		0.00211
(1.00) 		0.024
(1.00) 		0.00243
(1.00) 		0.00157
(1.00)
18q gain 105 (21%) 385 0.00884
(1.00) 		0.0236
(1.00) 		3.96e-07
(0.000365) 		0.00195
(1.00) 		0.405
(1.00) 		0.249
(1.00) 		0.000422
(0.353) 		1.63e-05
(0.0145) 		0.0487
(1.00) 		0.00534
(1.00) 		0.0837
(1.00) 		0.0245
(1.00)
19p gain 109 (22%) 381 0.037
(1.00) 		0.136
(1.00) 		7.25e-09
(6.75e-06) 		0.000253
(0.215) 		0.0183
(1.00) 		0.0391
(1.00) 		0.0019
(1.00) 		0.000322
(0.271) 		0.0223
(1.00) 		0.00143
(1.00) 		0.0363
(1.00) 		0.0893
(1.00)
7q loss 51 (10%) 439 0.162
(1.00) 		0.0175
(1.00) 		0.0308
(1.00) 		0.211
(1.00) 		0.93
(1.00) 		0.087
(1.00) 		0.000113
(0.0976) 		8.78e-05
(0.0766) 		0.0531
(1.00) 		0.174
(1.00) 		0.82
(1.00) 		0.371
(1.00)
9p loss 304 (62%) 186 0.00743
(1.00) 		0.00227
(1.00) 		1.23e-05
(0.011) 		0.019
(1.00) 		0.202
(1.00) 		0.0584
(1.00) 		6.31e-07
(0.000579) 		0.0003
(0.254) 		0.0513
(1.00) 		0.00828
(1.00) 		0.165
(1.00) 		0.493
(1.00)
19p loss 164 (33%) 326 0.0521
(1.00) 		0.00272
(1.00) 		1.36e-05
(0.0121) 		0.573
(1.00) 		0.832
(1.00) 		0.424
(1.00) 		0.125
(1.00) 		0.0203
(1.00) 		0.0325
(1.00) 		0.000236
(0.201) 		0.752
(1.00) 		0.906
(1.00)
2q gain 136 (28%) 354 0.35
(1.00) 		0.359
(1.00) 		5.74e-05
(0.0504) 		0.0313
(1.00) 		0.441
(1.00) 		0.487
(1.00) 		0.00278
(1.00) 		0.00623
(1.00) 		0.101
(1.00) 		0.0829
(1.00) 		0.00513
(1.00) 		0.109
(1.00)
4p gain 30 (6%) 460 0.326
(1.00) 		0.238
(1.00) 		2.55e-05
(0.0226) 		0.146
(1.00) 		0.277
(1.00) 		0.148
(1.00) 		0.0208
(1.00) 		0.0203
(1.00) 		0.255
(1.00) 		0.221
(1.00) 		0.205
(1.00) 		0.0371
(1.00)
12q gain 151 (31%) 339 0.0237
(1.00) 		0.325
(1.00) 		9.23e-07
(0.000846) 		0.00214
(1.00) 		0.507
(1.00) 		0.598
(1.00) 		0.00517
(1.00) 		0.00111
(0.896) 		0.286
(1.00) 		0.044
(1.00) 		0.00043
(0.36) 		0.0849
(1.00)
15q gain 104 (21%) 386 0.825
(1.00) 		0.551
(1.00) 		0.00204
(1.00) 		0.00182
(1.00) 		0.225
(1.00) 		0.779
(1.00) 		0.000651
(0.535) 		0.000264
(0.223) 		0.0123
(1.00) 		0.00151
(1.00) 		0.0243
(1.00) 		0.00577
(1.00)
19q gain 155 (32%) 335 0.113
(1.00) 		0.214
(1.00) 		0.000115
(0.0993) 		0.00978
(1.00) 		0.225
(1.00) 		0.102
(1.00) 		0.0595
(1.00) 		0.00408
(1.00) 		0.592
(1.00) 		0.319
(1.00) 		0.0774
(1.00) 		0.553
(1.00)
20p gain 254 (52%) 236 0.0198
(1.00) 		0.151
(1.00) 		4.93e-07
(0.000453) 		0.000596
(0.494) 		0.875
(1.00) 		0.201
(1.00) 		0.103
(1.00) 		0.00908
(1.00) 		0.066
(1.00) 		0.919
(1.00) 		0.404
(1.00) 		0.659
(1.00)
20q gain 243 (50%) 247 0.653
(1.00) 		0.48
(1.00) 		0.000131
(0.112) 		0.147
(1.00) 		0.467
(1.00) 		0.496
(1.00) 		0.441
(1.00) 		0.266
(1.00) 		0.0589
(1.00) 		0.00557
(1.00) 		0.459
(1.00) 		1
(1.00)
xq gain 77 (16%) 413 0.359
(1.00) 		0.731
(1.00) 		5.78e-05
(0.0507) 		0.00533
(1.00) 		0.696
(1.00) 		0.389
(1.00) 		0.00769
(1.00) 		0.0253
(1.00) 		0.00167
(1.00) 		0.165
(1.00) 		0.021
(1.00) 		0.0689
(1.00)
20q loss 46 (9%) 444 0.058
(1.00) 		0.182
(1.00) 		0.00642
(1.00) 		0.0508
(1.00) 		0.246
(1.00) 		0.3
(1.00) 		0.000361
(0.303) 		0.000243
(0.207) 		0.128
(1.00) 		0.587
(1.00) 		0.172
(1.00) 		0.549
(1.00)
21q loss 260 (53%) 230 0.89
(1.00) 		0.587
(1.00) 		1.55e-06
(0.00142) 		0.0364
(1.00) 		0.495
(1.00) 		0.504
(1.00) 		0.0948
(1.00) 		0.00581
(1.00) 		0.00201
(1.00) 		0.0401
(1.00) 		0.191
(1.00) 		0.015
(1.00)
22q loss 95 (19%) 395 0.00944
(1.00) 		0.0972
(1.00) 		0.109
(1.00) 		0.0402
(1.00) 		0.24
(1.00) 		0.0194
(1.00) 		0.000273
(0.231) 		0.000543
(0.452) 		0.299
(1.00) 		0.047
(1.00) 		0.673
(1.00) 		0.777
(1.00)
1p gain 88 (18%) 402 0.0877
(1.00) 		0.108
(1.00) 		0.326
(1.00) 		0.445
(1.00) 		0.482
(1.00) 		0.305
(1.00) 		0.745
(1.00) 		0.0312
(1.00) 		0.789
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.88
(1.00)
3p gain 107 (22%) 383 0.972
(1.00) 		0.318
(1.00) 		0.151
(1.00) 		0.0374
(1.00) 		0.834
(1.00) 		0.243
(1.00) 		0.175
(1.00) 		0.144
(1.00) 		0.776
(1.00) 		0.626
(1.00) 		0.674
(1.00) 		0.691
(1.00)
3q gain 307 (63%) 183 0.588
(1.00) 		0.336
(1.00) 		0.00239
(1.00) 		0.309
(1.00) 		1
(1.00) 		0.26
(1.00) 		0.229
(1.00) 		0.0308
(1.00) 		0.11
(1.00) 		0.118
(1.00) 		0.978
(1.00) 		0.255
(1.00)
4q gain 22 (4%) 468 0.585
(1.00) 		0.608
(1.00) 		0.0057
(1.00) 		0.112
(1.00) 		0.678
(1.00) 		0.134
(1.00) 		0.763
(1.00) 		0.706
(1.00) 		0.755
(1.00) 		0.513
(1.00) 		0.433
(1.00) 		0.558
(1.00)
5p gain 304 (62%) 186 0.749
(1.00) 		0.86
(1.00) 		0.000822
(0.672) 		0.795
(1.00) 		0.382
(1.00) 		0.577
(1.00) 		0.354
(1.00) 		0.732
(1.00) 		0.934
(1.00) 		0.0664
(1.00) 		0.339
(1.00) 		0.138
(1.00)
5q gain 93 (19%) 397 0.12
(1.00) 		0.168
(1.00) 		0.0335
(1.00) 		0.184
(1.00) 		0.475
(1.00) 		0.115
(1.00) 		0.176
(1.00) 		0.201
(1.00) 		0.0402
(1.00) 		0.118
(1.00) 		0.168
(1.00) 		0.678
(1.00)
6p gain 106 (22%) 384 0.0549
(1.00) 		0.262
(1.00) 		0.00148
(1.00) 		0.934
(1.00) 		0.921
(1.00) 		0.271
(1.00) 		0.00759
(1.00) 		0.00966
(1.00) 		0.749
(1.00) 		0.462
(1.00) 		0.738
(1.00) 		0.789
(1.00)
6q gain 91 (19%) 399 0.0698
(1.00) 		0.216
(1.00) 		0.000639
(0.527) 		0.504
(1.00) 		0.923
(1.00) 		0.938
(1.00) 		0.0208
(1.00) 		0.00318
(1.00) 		0.647
(1.00) 		0.542
(1.00) 		0.971
(1.00) 		0.673
(1.00)
8p gain 123 (25%) 367 0.591
(1.00) 		0.571
(1.00) 		0.227
(1.00) 		0.1
(1.00) 		0.559
(1.00) 		0.833
(1.00) 		0.092
(1.00) 		0.018
(1.00) 		0.505
(1.00) 		0.876
(1.00) 		1
(1.00) 		0.302
(1.00)
8q gain 247 (50%) 243 0.0491
(1.00) 		0.0764
(1.00) 		0.0413
(1.00) 		0.00742
(1.00) 		0.222
(1.00) 		0.959
(1.00) 		0.013
(1.00) 		0.0354
(1.00) 		0.0269
(1.00) 		0.124
(1.00) 		0.219
(1.00) 		0.268
(1.00)
10p gain 76 (16%) 414 0.323
(1.00) 		0.775
(1.00) 		0.0676
(1.00) 		0.162
(1.00) 		0.063
(1.00) 		0.0571
(1.00) 		0.126
(1.00) 		0.485
(1.00) 		0.0265
(1.00) 		0.000546
(0.455) 		0.484
(1.00) 		0.657
(1.00)
10q gain 43 (9%) 447 0.113
(1.00) 		0.248
(1.00) 		0.0821
(1.00) 		0.588
(1.00) 		0.0273
(1.00) 		0.184
(1.00) 		0.131
(1.00) 		0.126
(1.00) 		0.286
(1.00) 		0.176
(1.00) 		0.588
(1.00) 		0.854
(1.00)
11p gain 72 (15%) 418 0.68
(1.00) 		1
(1.00) 		0.0427
(1.00) 		0.22
(1.00) 		0.341
(1.00) 		0.00297
(1.00) 		0.768
(1.00) 		0.909
(1.00) 		0.0109
(1.00) 		0.407
(1.00) 		0.117
(1.00) 		0.873
(1.00)
11q gain 89 (18%) 401 0.0189
(1.00) 		0.115
(1.00) 		0.000634
(0.523) 		0.419
(1.00) 		0.399
(1.00) 		0.00256
(1.00) 		0.19
(1.00) 		0.027
(1.00) 		0.0568
(1.00) 		0.508
(1.00) 		0.146
(1.00) 		0.667
(1.00)
13q gain 39 (8%) 451 0.701
(1.00) 		0.455
(1.00) 		0.459
(1.00) 		0.857
(1.00) 		0.43
(1.00) 		0.815
(1.00) 		0.527
(1.00) 		0.846
(1.00) 		0.229
(1.00) 		0.781
(1.00) 		0.43
(1.00) 		0.135
(1.00)
14q gain 124 (25%) 366 0.143
(1.00) 		0.264
(1.00) 		0.227
(1.00) 		0.112
(1.00) 		0.248
(1.00) 		0.12
(1.00) 		0.0533
(1.00) 		0.0156
(1.00) 		0.00244
(1.00) 		0.0353
(1.00) 		0.202
(1.00) 		1
(1.00)
16p gain 86 (18%) 404 0.355
(1.00) 		0.0449
(1.00) 		0.0429
(1.00) 		0.502
(1.00) 		0.605
(1.00) 		0.879
(1.00) 		0.658
(1.00) 		0.138
(1.00) 		0.0495
(1.00) 		0.493
(1.00) 		0.00165
(1.00) 		0.293
(1.00)
16q gain 85 (17%) 405 0.921
(1.00) 		0.377
(1.00) 		0.0181
(1.00) 		0.332
(1.00) 		0.694
(1.00) 		0.463
(1.00) 		0.147
(1.00) 		0.0977
(1.00) 		0.151
(1.00) 		0.885
(1.00) 		0.0953
(1.00) 		0.176
(1.00)
21q gain 56 (11%) 434 0.888
(1.00) 		0.829
(1.00) 		0.743
(1.00) 		0.0649
(1.00) 		0.365
(1.00) 		0.901
(1.00) 		0.583
(1.00) 		0.909
(1.00) 		0.216
(1.00) 		0.577
(1.00) 		0.299
(1.00) 		1
(1.00)
22q gain 218 (44%) 272 0.00777
(1.00) 		0.0394
(1.00) 		0.00488
(1.00) 		0.0385
(1.00) 		0.946
(1.00) 		0.0467
(1.00) 		0.00383
(1.00) 		0.0149
(1.00) 		0.0722
(1.00) 		0.215
(1.00) 		0.0865
(1.00) 		0.504
(1.00)
1q loss 57 (12%) 433 0.554
(1.00) 		0.401
(1.00) 		0.000444
(0.371) 		0.0841
(1.00) 		1
(1.00) 		0.584
(1.00) 		0.0278
(1.00) 		0.0228
(1.00) 		0.3
(1.00) 		0.243
(1.00) 		0.673
(1.00) 		0.0141
(1.00)
2p loss 21 (4%) 469 0.0462
(1.00) 		0.111
(1.00) 		0.0344
(1.00) 		0.151
(1.00) 		0.14
(1.00) 		0.113
(1.00) 		0.622
(1.00) 		0.0351
(1.00) 		0.00405
(1.00) 		0.663
(1.00) 		0.0283
(1.00) 		0.0145
(1.00)
2q loss 41 (8%) 449 0.493
(1.00) 		0.664
(1.00) 		0.0968
(1.00) 		0.337
(1.00) 		0.881
(1.00) 		0.393
(1.00) 		0.294
(1.00) 		0.00302
(1.00) 		0.000344
(0.29) 		0.774
(1.00) 		0.00779
(1.00) 		0.00855
(1.00)
3p loss 303 (62%) 187 0.606
(1.00) 		0.68
(1.00) 		0.126
(1.00) 		0.00102
(0.828) 		0.936
(1.00) 		0.407
(1.00) 		0.321
(1.00) 		0.2
(1.00) 		0.0793
(1.00) 		0.21
(1.00) 		0.0528
(1.00) 		0.0403
(1.00)
3q loss 71 (14%) 419 0.926
(1.00) 		0.498
(1.00) 		0.472
(1.00) 		0.651
(1.00) 		0.471
(1.00) 		0.727
(1.00) 		0.893
(1.00) 		0.916
(1.00) 		0.924
(1.00) 		0.459
(1.00) 		0.0489
(1.00) 		0.0524
(1.00)
5p loss 76 (16%) 414 0.638
(1.00) 		0.307
(1.00) 		0.0652
(1.00) 		0.00161
(1.00) 		0.463
(1.00) 		0.0764
(1.00) 		0.27
(1.00) 		0.638
(1.00) 		0.187
(1.00) 		0.814
(1.00) 		0.347
(1.00) 		0.00836
(1.00)
5q loss 284 (58%) 206 0.166
(1.00) 		0.143
(1.00) 		0.00134
(1.00) 		0.00666
(1.00) 		0.109
(1.00) 		0.0687
(1.00) 		0.00881
(1.00) 		0.0049
(1.00) 		0.00935
(1.00) 		0.00668
(1.00) 		0.156
(1.00) 		0.0334
(1.00)
6q loss 109 (22%) 381 0.00524
(1.00) 		0.00539
(1.00) 		0.00146
(1.00) 		0.000963
(0.783) 		0.556
(1.00) 		0.385
(1.00) 		0.00138
(1.00) 		0.00127
(1.00) 		0.122
(1.00) 		0.254
(1.00) 		0.145
(1.00) 		0.0448
(1.00)
7p loss 58 (12%) 432 0.55
(1.00) 		0.469
(1.00) 		0.000714
(0.586) 		0.272
(1.00) 		0.663
(1.00) 		0.13
(1.00) 		0.226
(1.00) 		0.0485
(1.00) 		0.416
(1.00) 		0.171
(1.00) 		0.825
(1.00) 		0.488
(1.00)
8p loss 237 (48%) 253 0.901
(1.00) 		0.955
(1.00) 		0.0713
(1.00) 		0.00209
(1.00) 		0.132
(1.00) 		0.222
(1.00) 		0.165
(1.00) 		0.0202
(1.00) 		0.0415
(1.00) 		0.907
(1.00) 		0.37
(1.00) 		0.184
(1.00)
8q loss 49 (10%) 441 0.348
(1.00) 		0.178
(1.00) 		0.264
(1.00) 		0.00317
(1.00) 		0.0421
(1.00) 		0.616
(1.00) 		0.213
(1.00) 		0.0719
(1.00) 		0.435
(1.00) 		0.075
(1.00) 		0.802
(1.00) 		0.298
(1.00)
11p loss 168 (34%) 322 0.248
(1.00) 		0.0814
(1.00) 		0.00281
(1.00) 		0.00374
(1.00) 		0.13
(1.00) 		0.00041
(0.343) 		0.169
(1.00) 		0.0938
(1.00) 		0.385
(1.00) 		0.144
(1.00) 		0.112
(1.00) 		0.101
(1.00)
11q loss 139 (28%) 351 0.983
(1.00) 		0.933
(1.00) 		0.0023
(1.00) 		0.00144
(1.00) 		0.541
(1.00) 		0.732
(1.00) 		0.28
(1.00) 		0.157
(1.00) 		0.0181
(1.00) 		0.952
(1.00) 		0.215
(1.00) 		0.0693
(1.00)
12p loss 38 (8%) 452 0.0235
(1.00) 		0.0366
(1.00) 		0.303
(1.00) 		0.874
(1.00) 		0.0987
(1.00) 		0.826
(1.00) 		0.961
(1.00) 		0.206
(1.00) 		0.137
(1.00) 		0.0378
(1.00) 		0.583
(1.00) 		0.161
(1.00)
12q loss 48 (10%) 442 0.368
(1.00) 		0.32
(1.00) 		0.963
(1.00) 		0.693
(1.00) 		0.0267
(1.00) 		0.485
(1.00) 		0.788
(1.00) 		0.401
(1.00) 		0.182
(1.00) 		0.00987
(1.00) 		0.526
(1.00) 		0.724
(1.00)
13q loss 305 (62%) 185 0.614
(1.00) 		0.758
(1.00) 		0.0164
(1.00) 		0.0532
(1.00) 		0.701
(1.00) 		0.573
(1.00) 		0.203
(1.00) 		0.088
(1.00) 		0.312
(1.00) 		0.132
(1.00) 		0.0015
(1.00) 		0.00889
(1.00)
15q loss 137 (28%) 353 0.72
(1.00) 		0.242
(1.00) 		0.249
(1.00) 		0.0523
(1.00) 		0.325
(1.00) 		0.00258
(1.00) 		0.0714
(1.00) 		0.0102
(1.00) 		0.0482
(1.00) 		0.153
(1.00) 		0.0113
(1.00) 		0.901
(1.00)
16p loss 155 (32%) 335 0.9
(1.00) 		0.829
(1.00) 		0.00117
(0.939) 		0.121
(1.00) 		0.126
(1.00) 		0.479
(1.00) 		0.437
(1.00) 		0.406
(1.00) 		0.0914
(1.00) 		0.306
(1.00) 		0.0915
(1.00) 		0.239
(1.00)
16q loss 177 (36%) 313 0.762
(1.00) 		0.631
(1.00) 		0.0051
(1.00) 		0.162
(1.00) 		0.13
(1.00) 		0.816
(1.00) 		0.0455
(1.00) 		0.026
(1.00) 		0.0127
(1.00) 		0.0312
(1.00) 		0.0037
(1.00) 		0.0217
(1.00)
17p loss 285 (58%) 205 0.0051
(1.00) 		0.31
(1.00) 		0.00137
(1.00) 		0.0108
(1.00) 		0.438
(1.00) 		0.0077
(1.00) 		0.00031
(0.262) 		0.00571
(1.00) 		0.0282
(1.00) 		0.009
(1.00) 		0.696
(1.00) 		0.911
(1.00)
18p loss 139 (28%) 351 0.847
(1.00) 		0.6
(1.00) 		0.0187
(1.00) 		0.0841
(1.00) 		0.615
(1.00) 		0.933
(1.00) 		0.176
(1.00) 		0.0654
(1.00) 		0.387
(1.00) 		0.018
(1.00) 		0.00804
(1.00) 		0.538
(1.00)
18q loss 182 (37%) 308 0.175
(1.00) 		0.109
(1.00) 		0.0795
(1.00) 		0.323
(1.00) 		0.641
(1.00) 		0.767
(1.00) 		0.424
(1.00) 		0.00693
(1.00) 		0.205
(1.00) 		0.0381
(1.00) 		0.0592
(1.00) 		0.82
(1.00)
19q loss 110 (22%) 380 0.602
(1.00) 		0.171
(1.00) 		0.00999
(1.00) 		0.0482
(1.00) 		0.345
(1.00) 		0.922
(1.00) 		0.63
(1.00) 		0.831
(1.00) 		0.281
(1.00) 		0.143
(1.00) 		0.605
(1.00) 		0.294
(1.00)
20p loss 41 (8%) 449 0.143
(1.00) 		0.438
(1.00) 		0.0028
(1.00) 		0.00768
(1.00) 		0.114
(1.00) 		0.224
(1.00) 		0.195
(1.00) 		0.16
(1.00) 		0.0514
(1.00) 		0.717
(1.00) 		0.213
(1.00) 		0.403
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 0.000182 (Fisher's exact test), Q value = 0.16

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
1Q GAIN MUTATED 68 87 44
1Q GAIN WILD-TYPE 125 75 91

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 5.66e-05 (Fisher's exact test), Q value = 0.05

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
1Q GAIN MUTATED 39 62 36
1Q GAIN WILD-TYPE 103 52 64

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000129 (Fisher's exact test), Q value = 0.11

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
1Q GAIN MUTATED 42 75 79
1Q GAIN WILD-TYPE 51 65 167

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1.09e-11 (Fisher's exact test), Q value = 1e-08

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
2P GAIN MUTATED 56 107 55
2P GAIN WILD-TYPE 137 55 80

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 4.28e-06 (Fisher's exact test), Q value = 0.0039

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
2P GAIN MUTATED 49 74 42
2P GAIN WILD-TYPE 93 40 58

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.0012

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
2P GAIN MUTATED 39 88 63 22
2P GAIN WILD-TYPE 79 55 80 53

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.22e-05 (Fisher's exact test), Q value = 0.028

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
2P GAIN MUTATED 39 84 89
2P GAIN WILD-TYPE 54 56 157

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 5.74e-05 (Fisher's exact test), Q value = 0.05

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
2Q GAIN MUTATED 37 65 34
2Q GAIN WILD-TYPE 156 97 101

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 2.55e-05 (Fisher's exact test), Q value = 0.023

Table S9.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
4P GAIN MUTATED 9 2 19
4P GAIN WILD-TYPE 184 160 116

Figure S9.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
7P GAIN MUTATED 74 101 59
7P GAIN WILD-TYPE 119 61 76

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

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.000158 (Fisher's exact test), Q value = 0.14

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
7P GAIN MUTATED 50 70 46
7P GAIN WILD-TYPE 92 44 54

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.000119 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
7P GAIN MUTATED 53 90 58 27
7P GAIN WILD-TYPE 65 53 85 48

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

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.01e-07 (Fisher's exact test), Q value = 0.00055

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
7P GAIN MUTATED 31 92 105
7P GAIN WILD-TYPE 62 48 141

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 2.64e-11 (Fisher's exact test), Q value = 2.5e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
7Q GAIN MUTATED 55 105 54
7Q GAIN WILD-TYPE 138 57 81

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

'7q gain' versus 'METHLYATION_CNMF'

P value = 3.22e-07 (Fisher's exact test), Q value = 3e-04

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
7Q GAIN MUTATED 38 69 42
7Q GAIN WILD-TYPE 104 45 58

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 4.4e-09 (Fisher's exact test), Q value = 4.1e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
7Q GAIN MUTATED 45 94 43 28
7Q GAIN WILD-TYPE 73 49 100 47

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.38e-10 (Fisher's exact test), Q value = 6.9e-07

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
7Q GAIN MUTATED 28 93 89
7Q GAIN WILD-TYPE 65 47 157

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000128 (Fisher's exact test), Q value = 0.11

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
7Q GAIN MUTATED 48 67 92
7Q GAIN WILD-TYPE 23 96 138

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.094

Table S19.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
9P GAIN MUTATED 19 34 7
9P GAIN WILD-TYPE 174 128 128

Figure S19.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 9.67e-05 (Fisher's exact test), Q value = 0.084

Table S20.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
9P GAIN MUTATED 10 28 8
9P GAIN WILD-TYPE 132 86 92

Figure S20.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 7.21e-06 (Fisher's exact test), Q value = 0.0065

Table S21.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
9P GAIN MUTATED 5 35 13 7
9P GAIN WILD-TYPE 113 108 130 68

Figure S21.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.86e-07 (Fisher's exact test), Q value = 9e-04

Table S22.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
9P GAIN MUTATED 10 35 15
9P GAIN WILD-TYPE 83 105 231

Figure S22.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 2.89e-12 (Fisher's exact test), Q value = 2.7e-09

Table S23.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
9Q GAIN MUTATED 22 60 9
9Q GAIN WILD-TYPE 171 102 126

Figure S23.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 2.57e-10 (Fisher's exact test), Q value = 2.4e-07

Table S24.  Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
9Q GAIN MUTATED 10 44 11
9Q GAIN WILD-TYPE 132 70 89

Figure S24.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 4.94e-14 (Fisher's exact test), Q value = 4.7e-11

Table S25.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
9Q GAIN MUTATED 6 58 21 5
9Q GAIN WILD-TYPE 112 85 122 70

Figure S25.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.48e-16 (Fisher's exact test), Q value = 6.2e-13

Table S26.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
9Q GAIN MUTATED 14 59 17
9Q GAIN WILD-TYPE 79 81 229

Figure S26.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 4.34e-05 (Fisher's exact test), Q value = 0.038

Table S27.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
9Q GAIN MUTATED 32 19 12 24
9Q GAIN WILD-TYPE 113 111 113 40

Figure S27.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 5.25e-10 (Fisher's exact test), Q value = 4.9e-07

Table S28.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
12P GAIN MUTATED 54 98 72
12P GAIN WILD-TYPE 139 64 63

Figure S28.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 6.62e-05 (Fisher's exact test), Q value = 0.058

Table S29.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
12P GAIN MUTATED 38 81 75 26
12P GAIN WILD-TYPE 80 62 68 49

Figure S29.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 9.23e-07 (Fisher's exact test), Q value = 0.00085

Table S30.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
12Q GAIN MUTATED 37 73 41
12Q GAIN WILD-TYPE 156 89 94

Figure S30.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000264 (Fisher's exact test), Q value = 0.22

Table S31.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
15Q GAIN MUTATED 13 46 41
15Q GAIN WILD-TYPE 80 94 205

Figure S31.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1.7e-07 (Fisher's exact test), Q value = 0.00016

Table S32.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
17P GAIN MUTATED 9 40 16
17P GAIN WILD-TYPE 184 122 119

Figure S32.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.11

Table S33.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
17P GAIN MUTATED 8 35 15 6
17P GAIN WILD-TYPE 110 108 128 69

Figure S33.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.96e-05 (Fisher's exact test), Q value = 0.044

Table S34.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
17P GAIN MUTATED 13 33 18
17P GAIN WILD-TYPE 80 107 228

Figure S34.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.026

Table S35.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
17Q GAIN MUTATED 5 29 10 6
17Q GAIN WILD-TYPE 17 27 13 47

Figure S35.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1.51e-15 (Fisher's exact test), Q value = 1.4e-12

Table S36.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
17Q GAIN MUTATED 29 90 37
17Q GAIN WILD-TYPE 164 72 98

Figure S36.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 5.76e-10 (Fisher's exact test), Q value = 5.4e-07

Table S37.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
17Q GAIN MUTATED 23 62 30
17Q GAIN WILD-TYPE 119 52 70

Figure S37.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.99e-09 (Fisher's exact test), Q value = 1.9e-06

Table S38.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
17Q GAIN MUTATED 22 75 40 14
17Q GAIN WILD-TYPE 96 68 103 61

Figure S38.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.7e-10 (Fisher's exact test), Q value = 3.5e-07

Table S39.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
17Q GAIN MUTATED 30 73 48
17Q GAIN WILD-TYPE 63 67 198

Figure S39.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 3.5e-05 (Fisher's exact test), Q value = 0.031

Table S40.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
17Q GAIN MUTATED 46 55 20 24
17Q GAIN WILD-TYPE 99 75 105 40

Figure S40.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.38e-07 (Fisher's exact test), Q value = 0.00022

Table S41.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
17Q GAIN MUTATED 61 18 25
17Q GAIN WILD-TYPE 64 94 66

Figure S41.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.09e-06 (Fisher's exact test), Q value = 0.0046

Table S42.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 178 150
17Q GAIN MUTATED 37 67
17Q GAIN WILD-TYPE 141 83

Figure S42.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 5.05e-09 (Fisher's exact test), Q value = 4.7e-06

Table S43.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
18P GAIN MUTATED 36 78 33
18P GAIN WILD-TYPE 157 84 102

Figure S43.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 3e-06 (Fisher's exact test), Q value = 0.0027

Table S44.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
18P GAIN MUTATED 24 52 33
18P GAIN WILD-TYPE 118 62 67

Figure S44.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 3.96e-07 (Fisher's exact test), Q value = 0.00037

Table S45.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
18Q GAIN MUTATED 24 58 23
18Q GAIN WILD-TYPE 169 104 112

Figure S45.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.015

Table S46.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
18Q GAIN MUTATED 25 44 31
18Q GAIN WILD-TYPE 68 96 215

Figure S46.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 7.25e-09 (Fisher's exact test), Q value = 6.7e-06

Table S47.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
19P GAIN MUTATED 30 63 16
19P GAIN WILD-TYPE 163 99 119

Figure S47.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.000253 (Fisher's exact test), Q value = 0.21

Table S48.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
19P GAIN MUTATED 23 43 20
19P GAIN WILD-TYPE 119 71 80

Figure S48.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.099

Table S49.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
19Q GAIN MUTATED 44 71 40
19Q GAIN WILD-TYPE 149 91 95

Figure S49.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 4.93e-07 (Fisher's exact test), Q value = 0.00045

Table S50.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
20P GAIN MUTATED 73 107 74
20P GAIN WILD-TYPE 120 55 61

Figure S50.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.11

Table S51.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
20Q GAIN MUTATED 75 84 84
20Q GAIN WILD-TYPE 118 78 51

Figure S51.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 5.78e-05 (Fisher's exact test), Q value = 0.051

Table S52.  Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
XQ GAIN MUTATED 15 40 22
XQ GAIN WILD-TYPE 178 122 113

Figure S52.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.014

Table S53.  Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
1P LOSS MUTATED 8 30 8 3
1P LOSS WILD-TYPE 34 22 24 25

Figure S53.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.0017

Table S54.  Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
1P LOSS MUTATED 7 32 4 6
1P LOSS WILD-TYPE 15 24 19 47

Figure S54.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1.17e-20 (Fisher's exact test), Q value = 1.1e-17

Table S55.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
1P LOSS MUTATED 32 95 20
1P LOSS WILD-TYPE 161 67 115

Figure S55.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 2.16e-10 (Fisher's exact test), Q value = 2e-07

Table S56.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
1P LOSS MUTATED 20 59 24
1P LOSS WILD-TYPE 122 55 76

Figure S56.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.56e-12 (Fisher's exact test), Q value = 1.5e-09

Table S57.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
1P LOSS MUTATED 21 79 28 17
1P LOSS WILD-TYPE 97 64 115 58

Figure S57.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.66e-13 (Fisher's exact test), Q value = 2.5e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
1P LOSS MUTATED 18 78 49
1P LOSS WILD-TYPE 75 62 197

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

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.16

Table S59.  Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
1P LOSS MUTATED 44 41 22 31
1P LOSS WILD-TYPE 101 89 103 33

Figure S59.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.55e-05 (Fisher's exact test), Q value = 0.057

Table S60.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
1P LOSS MUTATED 37 45 56
1P LOSS WILD-TYPE 34 118 174

Figure S60.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 6.51e-13 (Fisher's exact test), Q value = 6.2e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
4P LOSS MUTATED 90 136 81
4P LOSS WILD-TYPE 103 26 54

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

'4p loss' versus 'METHLYATION_CNMF'

P value = 8.23e-08 (Fisher's exact test), Q value = 7.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
4P LOSS MUTATED 64 90 67
4P LOSS WILD-TYPE 78 24 33

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

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1.74e-06 (Fisher's exact test), Q value = 0.0016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
4P LOSS MUTATED 77 113 74 38
4P LOSS WILD-TYPE 41 30 69 37

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

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.08e-06 (Fisher's exact test), Q value = 0.0028

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
4P LOSS MUTATED 58 111 133
4P LOSS WILD-TYPE 35 29 113

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

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.000121 (Fisher's exact test), Q value = 0.1

Table S65.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
4P LOSS MUTATED 97 92 58 46
4P LOSS WILD-TYPE 48 38 67 18

Figure S65.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.098

Table S66.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
4P LOSS MUTATED 96 60 49
4P LOSS WILD-TYPE 29 52 42

Figure S66.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.011

Table S67.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 178 150
4P LOSS MUTATED 92 113
4P LOSS WILD-TYPE 86 37

Figure S67.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 5.18e-11 (Fisher's exact test), Q value = 4.9e-08

Table S68.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
4Q LOSS MUTATED 91 130 69
4Q LOSS WILD-TYPE 102 32 66

Figure S68.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3.28e-05 (Fisher's exact test), Q value = 0.029

Table S69.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
4Q LOSS MUTATED 68 86 57
4Q LOSS WILD-TYPE 74 28 43

Figure S69.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2.88e-06 (Fisher's exact test), Q value = 0.0026

Table S70.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
4Q LOSS MUTATED 67 109 77 32
4Q LOSS WILD-TYPE 51 34 66 43

Figure S70.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.13e-06 (Fisher's exact test), Q value = 0.0037

Table S71.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
4Q LOSS MUTATED 58 105 122
4Q LOSS WILD-TYPE 35 35 124

Figure S71.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.22

Table S72.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
6P LOSS MUTATED 31 54 24
6P LOSS WILD-TYPE 162 108 111

Figure S72.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 9.41e-05 (Fisher's exact test), Q value = 0.082

Table S73.  Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
6P LOSS MUTATED 20 42 20
6P LOSS WILD-TYPE 122 72 80

Figure S73.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 7.11e-06 (Fisher's exact test), Q value = 0.0064

Table S74.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
6P LOSS MUTATED 20 54 20 13
6P LOSS WILD-TYPE 98 89 123 62

Figure S74.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.58e-07 (Fisher's exact test), Q value = 0.00051

Table S75.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
6P LOSS MUTATED 12 54 41
6P LOSS WILD-TYPE 81 86 205

Figure S75.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.098

Table S76.  Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
7Q LOSS MUTATED 13 5 28 5
7Q LOSS WILD-TYPE 105 138 115 70

Figure S76.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.78e-05 (Fisher's exact test), Q value = 0.077

Table S77.  Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
7Q LOSS MUTATED 20 5 26
7Q LOSS WILD-TYPE 73 135 220

Figure S77.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.011

Table S78.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
9P LOSS MUTATED 109 89 106
9P LOSS WILD-TYPE 84 73 29

Figure S78.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 6.31e-07 (Fisher's exact test), Q value = 0.00058

Table S79.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
9P LOSS MUTATED 91 68 99 38
9P LOSS WILD-TYPE 27 75 44 37

Figure S79.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.01

Table S80.  Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
9Q LOSS MUTATED 28 11 21 13
9Q LOSS WILD-TYPE 14 41 11 15

Figure S80.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 7.37e-06 (Fisher's exact test), Q value = 0.0066

Table S81.  Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
9Q LOSS MUTATED 12 12 17 32
9Q LOSS WILD-TYPE 10 44 6 21

Figure S81.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1.19e-17 (Fisher's exact test), Q value = 1.1e-14

Table S82.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
9Q LOSS MUTATED 100 39 100
9Q LOSS WILD-TYPE 93 123 35

Figure S82.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.75e-09 (Fisher's exact test), Q value = 1.6e-06

Table S83.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
9Q LOSS MUTATED 81 29 65
9Q LOSS WILD-TYPE 61 85 35

Figure S83.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 5.61e-20 (Fisher's exact test), Q value = 5.4e-17

Table S84.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
9Q LOSS MUTATED 81 24 88 40
9Q LOSS WILD-TYPE 37 119 55 35

Figure S84.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.03e-18 (Fisher's exact test), Q value = 4.8e-15

Table S85.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
9Q LOSS MUTATED 56 25 152
9Q LOSS WILD-TYPE 37 115 94

Figure S85.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 2.32e-08 (Fisher's exact test), Q value = 2.2e-05

Table S86.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
9Q LOSS MUTATED 62 80 71 12
9Q LOSS WILD-TYPE 83 50 54 52

Figure S86.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.77e-10 (Fisher's exact test), Q value = 3.6e-07

Table S87.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
9Q LOSS MUTATED 13 104 108
9Q LOSS WILD-TYPE 58 59 122

Figure S87.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 3.79e-06 (Fisher's exact test), Q value = 0.0034

Table S88.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
10P LOSS MUTATED 59 92 59
10P LOSS WILD-TYPE 134 70 76

Figure S88.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 2.74e-08 (Fisher's exact test), Q value = 2.5e-05

Table S89.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
10P LOSS MUTATED 40 73 37
10P LOSS WILD-TYPE 102 41 63

Figure S89.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1.35e-06 (Fisher's exact test), Q value = 0.0012

Table S90.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
10P LOSS MUTATED 43 88 49 24
10P LOSS WILD-TYPE 75 55 94 51

Figure S90.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.7e-08 (Fisher's exact test), Q value = 4.4e-05

Table S91.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
10P LOSS MUTATED 35 88 81
10P LOSS WILD-TYPE 58 52 165

Figure S91.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 6.47e-05 (Fisher's exact test), Q value = 0.057

Table S92.  Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
10P LOSS MUTATED 61 63 36 40
10P LOSS WILD-TYPE 84 67 89 24

Figure S92.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.012

Table S93.  Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
10P LOSS MUTATED 48 70 82
10P LOSS WILD-TYPE 23 93 148

Figure S93.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1.61e-06 (Fisher's exact test), Q value = 0.0015

Table S94.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
10Q LOSS MUTATED 64 98 61
10Q LOSS WILD-TYPE 129 64 74

Figure S94.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 3.67e-07 (Fisher's exact test), Q value = 0.00034

Table S95.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
10Q LOSS MUTATED 44 74 45
10Q LOSS WILD-TYPE 98 40 55

Figure S95.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 6.67e-09 (Fisher's exact test), Q value = 6.2e-06

Table S96.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
10Q LOSS MUTATED 47 96 51 23
10Q LOSS WILD-TYPE 71 47 92 52

Figure S96.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.16e-10 (Fisher's exact test), Q value = 6.7e-07

Table S97.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
10Q LOSS MUTATED 38 95 84
10Q LOSS WILD-TYPE 55 45 162

Figure S97.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.15

Table S98.  Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
10Q LOSS MUTATED 58 68 44 42
10Q LOSS WILD-TYPE 87 62 81 22

Figure S98.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.34e-06 (Fisher's exact test), Q value = 0.0075

Table S99.  Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
10Q LOSS MUTATED 50 75 87
10Q LOSS WILD-TYPE 21 88 143

Figure S99.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 7.22e-05 (Fisher's exact test), Q value = 0.063

Table S100.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
14Q LOSS MUTATED 2 21 12 12
14Q LOSS WILD-TYPE 40 31 20 16

Figure S100.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 3.92e-10 (Fisher's exact test), Q value = 3.7e-07

Table S101.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
14Q LOSS MUTATED 17 62 67 14
14Q LOSS WILD-TYPE 101 81 76 61

Figure S101.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-12 (Fisher's exact test), Q value = 2.5e-09

Table S102.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
14Q LOSS MUTATED 52 62 46
14Q LOSS WILD-TYPE 41 78 200

Figure S102.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1.67e-07 (Fisher's exact test), Q value = 0.00015

Table S103.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
14Q LOSS MUTATED 46 37 30 42
14Q LOSS WILD-TYPE 99 93 95 22

Figure S103.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.77e-06 (Fisher's exact test), Q value = 0.0034

Table S104.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
14Q LOSS MUTATED 42 52 61
14Q LOSS WILD-TYPE 29 111 169

Figure S104.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.1

Table S105.  Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
17Q LOSS MUTATED 38 8 20
17Q LOSS WILD-TYPE 104 106 80

Figure S105.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.019

Table S106.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
17Q LOSS MUTATED 34 10 27 18
17Q LOSS WILD-TYPE 84 133 116 57

Figure S106.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0094

Table S107.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
17Q LOSS MUTATED 13 11 65
17Q LOSS WILD-TYPE 80 129 181

Figure S107.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.012

Table S108.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
19P LOSS MUTATED 48 49 67
19P LOSS WILD-TYPE 145 113 68

Figure S108.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000236 (Fisher's exact test), Q value = 0.2

Table S109.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 230
19P LOSS MUTATED 12 70 70
19P LOSS WILD-TYPE 59 93 160

Figure S109.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000243 (Fisher's exact test), Q value = 0.21

Table S110.  Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 246
20Q LOSS MUTATED 8 25 12
20Q LOSS WILD-TYPE 85 115 234

Figure S110.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.0014

Table S111.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
21Q LOSS MUTATED 75 105 80
21Q LOSS WILD-TYPE 118 57 55

Figure S111.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.23

Table S112.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 143 75
22Q LOSS MUTATED 23 14 43 14
22Q LOSS WILD-TYPE 95 129 100 61

Figure S112.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.000279 (Fisher's exact test), Q value = 0.24

Table S113.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
XQ LOSS MUTATED 27 39 44
XQ LOSS WILD-TYPE 166 123 91

Figure S113.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.84e-05 (Fisher's exact test), Q value = 0.077

Table S114.  Gene #80: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
XQ LOSS MUTATED 44 19 11
XQ LOSS WILD-TYPE 81 93 80

Figure S114.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000197 (Fisher's exact test), Q value = 0.17

Table S115.  Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 178 150
XQ LOSS MUTATED 26 48
XQ LOSS WILD-TYPE 152 102

Figure S115.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 490

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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