Correlation between copy number variations of arm-level result and molecular subtypes
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1P55MNV
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1P55MNV
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 82 arm-level events and 10 molecular subtypes across 295 patients, 220 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 2q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'RPPA_CHIERARCHICAL'.

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

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'RPPA_CNMF'.

  • 7p gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 8p gain cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 11p gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 12q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 13q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 18q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 20q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 22q gain cnv correlated to 'MRNASEQ_CNMF'.

  • xp gain cnv correlated to 'CN_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 1p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 2q loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

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

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

  • 5q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 6q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 7q loss cnv correlated to 'RPPA_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 8q loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'METHLYATION_CNMF'.

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

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

  • 15q loss cnv correlated to 'RPPA_CNMF'.

  • 16p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 17q loss cnv correlated to 'METHLYATION_CNMF'.

  • 18p loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 19q loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CNMF'.

  • 20q loss cnv correlated to 'RPPA_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • xp loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 220 significant findings detected.

Clinical
Features 		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
19p loss 60 (20%) 235 2e-05
(0.00205) 		0.00047
(0.0107) 		0.629
(0.786) 		0.28
(0.502) 		0.00155
(0.0205) 		0.00258
(0.0286) 		0.0296
(0.134) 		0.0002
(0.00607) 		0.0493
(0.184) 		0.015
(0.0957)
3q gain 175 (59%) 120 1e-05
(0.00137) 		7e-05
(0.00383) 		0.586
(0.769) 		0.32
(0.547) 		0.00133
(0.0188) 		3e-05
(0.00224) 		0.356
(0.576) 		0.00024
(0.00679) 		0.00325
(0.0346) 		0.00025
(0.00683)
5p gain 113 (38%) 182 1e-05
(0.00137) 		0.0185
(0.108) 		0.112
(0.301) 		0.838
(0.907) 		0.0356
(0.151) 		0.0147
(0.095) 		0.034
(0.149) 		0.00839
(0.0649) 		0.498
(0.7) 		0.0297
(0.134)
3p loss 82 (28%) 213 0.603
(0.771) 		0.00036
(0.00892) 		0.83
(0.9) 		0.058
(0.203) 		0.031
(0.139) 		0.00057
(0.0117) 		0.0258
(0.127) 		0.0037
(0.0379) 		0.00235
(0.0271) 		0.00103
(0.0164)
8q loss 24 (8%) 271 0.126
(0.326) 		0.00011
(0.00508) 		0.198
(0.425) 		0.043
(0.174) 		0.00012
(0.00508) 		6e-05
(0.00378) 		0.0171
(0.105) 		0.00022
(0.00644) 		0.462
(0.675) 		0.00148
(0.0202)
16q loss 44 (15%) 251 0.144
(0.356) 		0.00375
(0.038) 		0.0232
(0.12) 		0.107
(0.296) 		0.00174
(0.0217) 		0.00108
(0.0167) 		0.0094
(0.0701) 		0.00116
(0.0173) 		0.0879
(0.266) 		0.0141
(0.0932)
1p gain 90 (31%) 205 0.00891
(0.0683) 		0.00689
(0.0565) 		0.133
(0.341) 		0.748
(0.857) 		0.00036
(0.00892) 		0.00119
(0.0174) 		0.415
(0.637) 		0.00013
(0.00508) 		0.329
(0.557) 		0.0125
(0.085)
9q gain 47 (16%) 248 0.665
(0.809) 		5e-05
(0.00342) 		0.576
(0.764) 		0.556
(0.745) 		0.0108
(0.0759) 		0.00016
(0.00596) 		0.0248
(0.125) 		0.00307
(0.0331) 		0.29
(0.514) 		0.00057
(0.0117)
21q loss 49 (17%) 246 3e-05
(0.00224) 		0.0481
(0.18) 		0.538
(0.73) 		0.0246
(0.125) 		0.0179
(0.107) 		0.00398
(0.0393) 		0.305
(0.53) 		0.0255
(0.127) 		0.53
(0.725) 		0.772
(0.872)
1q gain 140 (47%) 155 7e-05
(0.00383) 		0.273
(0.494) 		0.107
(0.296) 		0.382
(0.608) 		0.00445
(0.0428) 		0.00713
(0.0579) 		0.486
(0.69) 		0.00384
(0.0384) 		0.156
(0.373) 		0.0103
(0.0753)
2p gain 64 (22%) 231 1e-05
(0.00137) 		0.0106
(0.0759) 		0.264
(0.491) 		0.12
(0.317) 		0.0146
(0.095) 		0.0405
(0.165) 		0.169
(0.387) 		0.00077
(0.0137) 		0.182
(0.406) 		0.388
(0.616)
7q gain 37 (13%) 258 0.0479
(0.18) 		0.00649
(0.0554) 		0.0054
(0.0481) 		0.137
(0.344) 		0.654
(0.802) 		0.238
(0.463) 		0.0009
(0.0154) 		0.191
(0.418) 		0.0106
(0.0759) 		0.0616
(0.209)
8q gain 91 (31%) 204 0.27
(0.492) 		0.0108
(0.0759) 		0.969
(0.987) 		0.499
(0.7) 		0.0181
(0.108) 		0.00131
(0.0188) 		0.166
(0.383) 		0.00684
(0.0565) 		0.616
(0.781) 		0.0002
(0.00607)
4p loss 131 (44%) 164 1e-05
(0.00137) 		0.0816
(0.254) 		0.471
(0.68) 		1
(1.00) 		0.00462
(0.0435) 		0.00174
(0.0217) 		0.392
(0.618) 		0.00082
(0.0143) 		1
(1.00) 		0.00047
(0.0107)
8p loss 82 (28%) 213 0.00012
(0.00508) 		0.108
(0.297) 		0.226
(0.445) 		0.222
(0.439) 		0.0193
(0.111) 		0.311
(0.536) 		0.0183
(0.108) 		0.0449
(0.176) 		0.011
(0.0763) 		0.0696
(0.229)
13q loss 80 (27%) 215 0.001
(0.0164) 		0.0303
(0.136) 		0.0784
(0.247) 		0.12
(0.317) 		0.0174
(0.106) 		0.0453
(0.177) 		0.102
(0.285) 		0.00343
(0.0361) 		0.638
(0.791) 		0.106
(0.296)
18q loss 73 (25%) 222 0.619
(0.784) 		0.00068
(0.0133) 		0.103
(0.289) 		0.206
(0.427) 		3e-05
(0.00224) 		0.00104
(0.0164) 		0.0823
(0.255) 		0.00018
(0.00607) 		0.0796
(0.25) 		0.0189
(0.11)
2q gain 37 (13%) 258 0.00013
(0.00508) 		0.162
(0.379) 		0.0601
(0.206) 		0.314
(0.54) 		0.0202
(0.113) 		0.00449
(0.0428) 		0.16
(0.377) 		0.00249
(0.028) 		0.158
(0.375) 		0.663
(0.808)
6p gain 52 (18%) 243 0.119
(0.317) 		0.021
(0.115) 		0.249
(0.478) 		0.00621
(0.0542) 		0.0257
(0.127) 		0.0711
(0.232) 		0.545
(0.738) 		0.0377
(0.159) 		0.306
(0.531) 		0.0973
(0.281)
7p gain 38 (13%) 257 0.211
(0.429) 		0.00358
(0.0372) 		0.00656
(0.0555) 		0.211
(0.429) 		0.0287
(0.134) 		0.404
(0.627) 		0.0005
(0.0108) 		0.0947
(0.277) 		0.0594
(0.205) 		0.137
(0.344)
9p gain 49 (17%) 246 0.646
(0.797) 		0.0465
(0.177) 		0.28
(0.502) 		0.0774
(0.246) 		0.332
(0.558) 		0.0111
(0.0763) 		0.332
(0.558) 		0.0177
(0.107) 		0.79
(0.879) 		0.0277
(0.133)
11q gain 8 (3%) 287 0.0191
(0.11) 		0.692
(0.819) 		0.135
(0.343) 		0.671
(0.812) 		0.0467
(0.177) 		0.0018
(0.0217) 		0.203
(0.426) 		0.0234
(0.12) 		0.267
(0.491) 		0.578
(0.766)
20q gain 115 (39%) 180 0.00476
(0.0437) 		0.143
(0.355) 		0.0048
(0.0437) 		0.00244
(0.0278) 		0.411
(0.634) 		0.055
(0.197) 		0.463
(0.675) 		0.0345
(0.149) 		0.806
(0.884) 		0.343
(0.565)
6q loss 74 (25%) 221 0.00468
(0.0436) 		0.00786
(0.0614) 		0.905
(0.948) 		0.603
(0.771) 		0.18
(0.405) 		0.0292
(0.134) 		0.21
(0.428) 		0.0352
(0.15) 		0.24
(0.466) 		0.161
(0.378)
12p loss 40 (14%) 255 0.0229
(0.119) 		0.0142
(0.0933) 		0.0003
(0.00794) 		0.00068
(0.0133) 		0.061
(0.209) 		0.489
(0.693) 		0.267
(0.491) 		0.802
(0.884) 		0.307
(0.532) 		0.204
(0.427)
xp loss 63 (21%) 232 0.00443
(0.0428) 		0.00265
(0.029) 		0.5
(0.7) 		0.822
(0.897) 		0.613
(0.779) 		0.889
(0.943) 		0.0249
(0.126) 		0.268
(0.491) 		0.0211
(0.115) 		0.264
(0.491)
8p gain 53 (18%) 242 0.778
(0.876) 		0.221
(0.438) 		0.64
(0.791) 		0.522
(0.717) 		0.0222
(0.117) 		0.0736
(0.238) 		0.72
(0.835) 		0.0269
(0.13) 		0.941
(0.971) 		0.0281
(0.134)
20p gain 100 (34%) 195 0.00074
(0.0135) 		0.00495
(0.0446) 		0.375
(0.598) 		0.0073
(0.0581) 		0.0918
(0.272) 		0.0657
(0.221) 		0.0513
(0.189) 		0.101
(0.285) 		0.659
(0.805) 		0.594
(0.771)
2q loss 35 (12%) 260 0.804
(0.884) 		0.329
(0.557) 		0.449
(0.661) 		0.432
(0.649) 		0.00924
(0.0695) 		0.048
(0.18) 		0.148
(0.362) 		0.0214
(0.115) 		0.865
(0.929) 		0.205
(0.427)
3q loss 14 (5%) 281 0.303
(0.53) 		0.0394
(0.164) 		0.917
(0.955) 		0.0289
(0.134) 		0.0205
(0.114) 		0.424
(0.645) 		0.0744
(0.239) 		0.372
(0.595) 		0.259
(0.486) 		0.151
(0.364)
5q loss 51 (17%) 244 0.00173
(0.0217) 		0.715
(0.832) 		0.4
(0.624) 		0.443
(0.657) 		0.392
(0.618) 		0.874
(0.933) 		0.029
(0.134) 		0.266
(0.491) 		0.429
(0.647) 		0.0443
(0.175)
9q loss 51 (17%) 244 0.00019
(0.00607) 		0.0444
(0.175) 		0.201
(0.426) 		0.494
(0.697) 		0.0901
(0.27) 		0.069
(0.228) 		0.472
(0.68) 		0.436
(0.652) 		0.00176
(0.0217) 		0.178
(0.401)
11p loss 100 (34%) 195 0.0015
(0.0202) 		0.305
(0.53) 		0.346
(0.568) 		0.026
(0.127) 		0.0325
(0.144) 		0.0862
(0.265) 		0.634
(0.789) 		0.0617
(0.209) 		0.949
(0.978) 		0.215
(0.434)
11q loss 115 (39%) 180 2e-05
(0.00205) 		0.399
(0.624) 		0.64
(0.791) 		0.293
(0.517) 		0.035
(0.15) 		0.0877
(0.266) 		0.723
(0.836) 		0.00727
(0.0581) 		0.805
(0.884) 		0.466
(0.676)
16p loss 34 (12%) 261 0.101
(0.285) 		0.0325
(0.144) 		0.0673
(0.224) 		0.389
(0.616) 		0.0285
(0.134) 		0.188
(0.417) 		0.41
(0.634) 		0.00997
(0.0737) 		0.0541
(0.195) 		0.199
(0.425)
18p loss 55 (19%) 240 0.393
(0.618) 		0.078
(0.247) 		0.286
(0.51) 		0.205
(0.427) 		0.0106
(0.0759) 		0.0381
(0.159) 		0.422
(0.645) 		0.0347
(0.149) 		0.3
(0.526) 		0.15
(0.364)
13q gain 24 (8%) 271 0.962
(0.983) 		0.47
(0.68) 		0.992
(1.00) 		0.696
(0.819) 		0.101
(0.285) 		0.0438
(0.174) 		0.00548
(0.0483) 		0.0672
(0.224) 		0.0991
(0.282) 		0.109
(0.298)
17p gain 22 (7%) 273 0.00074
(0.0135) 		0.00011
(0.00508) 		0.196
(0.422) 		0.973
(0.989) 		0.0801
(0.251) 		0.336
(0.559) 		0.249
(0.478) 		0.651
(0.8) 		0.0773
(0.246) 		0.505
(0.705)
17q gain 42 (14%) 253 0.0152
(0.0957) 		0.00904
(0.0686) 		0.45
(0.662) 		0.0568
(0.202) 		0.192
(0.418) 		0.394
(0.62) 		0.161
(0.378) 		0.808
(0.885) 		0.269
(0.491) 		0.784
(0.877)
18p gain 49 (17%) 246 0.0344
(0.149) 		0.355
(0.576) 		0.464
(0.675) 		0.765
(0.865) 		0.0402
(0.165) 		0.164
(0.381) 		0.922
(0.958) 		0.288
(0.512) 		0.785
(0.877) 		0.689
(0.819)
19q gain 72 (24%) 223 1e-05
(0.00137) 		0.166
(0.383) 		0.959
(0.983) 		0.783
(0.877) 		0.126
(0.326) 		0.0433
(0.174) 		0.68
(0.815) 		0.096
(0.279) 		0.816
(0.892) 		0.8
(0.884)
xq gain 42 (14%) 253 0.0215
(0.115) 		0.0345
(0.149) 		0.448
(0.661) 		0.429
(0.647) 		0.322
(0.549) 		0.227
(0.445) 		0.268
(0.491) 		0.201
(0.426) 		0.306
(0.531) 		0.278
(0.5)
1p loss 13 (4%) 282 0.0541
(0.195) 		0.0699
(0.229) 		0.473
(0.68) 		0.4
(0.624) 		0.00049
(0.0108) 		0.0194
(0.111) 		0.136
(0.343) 		0.199
(0.425) 		0.444
(0.658) 		0.674
(0.814)
1q loss 9 (3%) 286 0.0211
(0.115) 		0.25
(0.478) 		0.521
(0.717) 		0.683
(0.817) 		0.0413
(0.168) 		0.154
(0.37) 		0.0918
(0.272) 		0.44
(0.655) 		0.474
(0.68) 		0.739
(0.85)
4q loss 93 (32%) 202 1e-05
(0.00137) 		0.482
(0.686) 		0.157
(0.373) 		0.871
(0.932) 		0.0953
(0.278) 		0.0131
(0.0878) 		0.961
(0.983) 		0.0521
(0.191) 		0.0552
(0.197) 		0.668
(0.81)
6p loss 47 (16%) 248 0.151
(0.364) 		0.0399
(0.165) 		0.752
(0.86) 		0.277
(0.5) 		0.275
(0.497) 		0.0286
(0.134) 		0.448
(0.661) 		0.121
(0.319) 		0.897
(0.945) 		0.123
(0.322)
7p loss 26 (9%) 269 0.0464
(0.177) 		0.261
(0.489) 		0.425
(0.645) 		0.0933
(0.275) 		0.04
(0.165) 		0.251
(0.478) 		0.217
(0.436) 		0.825
(0.898) 		0.556
(0.745) 		0.0532
(0.194)
14q loss 35 (12%) 260 0.001
(0.0164) 		0.0819
(0.254) 		0.528
(0.724) 		0.089
(0.268) 		0.0902
(0.27) 		0.138
(0.346) 		0.851
(0.919) 		0.0992
(0.282) 		0.0151
(0.0957) 		0.627
(0.786)
20p loss 23 (8%) 272 0.788
(0.878) 		0.118
(0.313) 		0.0138
(0.0919) 		0.952
(0.979) 		0.0229
(0.119) 		0.0834
(0.257) 		0.114
(0.304) 		0.149
(0.363) 		0.135
(0.343) 		0.367
(0.588)
22q loss 71 (24%) 224 0.00227
(0.0266) 		0.73
(0.843) 		0.679
(0.815) 		0.115
(0.306) 		0.291
(0.516) 		0.0196
(0.111) 		0.911
(0.952) 		0.209
(0.428) 		0.628
(0.786) 		0.795
(0.883)
xq loss 59 (20%) 236 0.0458
(0.177) 		0.202
(0.426) 		0.64
(0.791) 		0.676
(0.815) 		0.604
(0.771) 		0.782
(0.877) 		0.15
(0.364) 		0.899
(0.945) 		0.0286
(0.134) 		0.424
(0.645)
3p gain 71 (24%) 224 0.512
(0.71) 		0.166
(0.383) 		0.58
(0.766) 		0.00665
(0.0556) 		0.695
(0.819) 		1
(1.00) 		0.434
(0.65) 		0.581
(0.766) 		0.426
(0.645) 		0.553
(0.745)
5q gain 44 (15%) 251 0.00192
(0.0228) 		0.622
(0.785) 		0.802
(0.884) 		1
(1.00) 		0.257
(0.485) 		0.785
(0.877) 		0.896
(0.945) 		0.957
(0.982) 		0.635
(0.789) 		0.875
(0.933)
6q gain 36 (12%) 259 0.13
(0.336) 		0.0874
(0.266) 		0.0219
(0.116) 		0.0914
(0.272) 		0.208
(0.427) 		0.198
(0.425) 		0.338
(0.559) 		0.192
(0.418) 		0.336
(0.559) 		0.208
(0.427)
11p gain 9 (3%) 286 0.764
(0.865) 		0.568
(0.758) 		0.244
(0.47) 		0.897
(0.945) 		0.377
(0.6) 		0.155
(0.371) 		0.631
(0.787) 		0.0206
(0.114) 		0.832
(0.902) 		0.805
(0.884)
12p gain 53 (18%) 242 0.241
(0.467) 		0.193
(0.418) 		0.0624
(0.21) 		0.721
(0.835) 		0.00634
(0.0547) 		0.669
(0.81) 		0.709
(0.828) 		0.352
(0.573) 		0.901
(0.945) 		0.9
(0.945)
12q gain 50 (17%) 245 0.176
(0.398) 		0.177
(0.399) 		0.11
(0.298) 		0.781
(0.877) 		0.0125
(0.085) 		0.329
(0.557) 		0.922
(0.958) 		0.273
(0.494) 		1
(1.00) 		0.881
(0.938)
14q gain 47 (16%) 248 0.0458
(0.177) 		0.829
(0.9) 		0.253
(0.48) 		0.225
(0.444) 		0.163
(0.381) 		1
(1.00) 		0.286
(0.51) 		0.147
(0.362) 		0.497
(0.7) 		0.988
(0.999)
16p gain 44 (15%) 251 0.00781
(0.0614) 		0.693
(0.819) 		0.747
(0.857) 		0.689
(0.819) 		0.446
(0.659) 		0.467
(0.677) 		0.0984
(0.282) 		0.097
(0.281) 		0.883
(0.939) 		0.583
(0.766)
18q gain 32 (11%) 263 0.133
(0.34) 		0.505
(0.705) 		0.434
(0.65) 		0.22
(0.437) 		0.0014
(0.0195) 		0.253
(0.479) 		0.336
(0.559) 		0.338
(0.559) 		0.428
(0.647) 		0.396
(0.62)
19p gain 44 (15%) 251 0.0167
(0.104) 		0.661
(0.807) 		0.605
(0.771) 		0.987
(0.999) 		0.587
(0.769) 		0.205
(0.427) 		0.936
(0.968) 		0.192
(0.418) 		0.634
(0.789) 		0.593
(0.771)
21q gain 37 (13%) 258 0.357
(0.576) 		0.35
(0.573) 		0.976
(0.99) 		0.717
(0.834) 		0.0171
(0.105) 		0.358
(0.577) 		0.753
(0.86) 		0.759
(0.864) 		0.924
(0.958) 		0.603
(0.771)
22q gain 29 (10%) 266 0.149
(0.363) 		0.757
(0.863) 		0.829
(0.9) 		0.582
(0.766) 		0.00017
(0.00606) 		0.25
(0.478) 		0.777
(0.876) 		0.331
(0.558) 		0.147
(0.362) 		0.961
(0.983)
xp gain 42 (14%) 253 0.0278
(0.133) 		0.123
(0.322) 		0.708
(0.828) 		0.352
(0.573) 		0.125
(0.326) 		0.0676
(0.224) 		0.601
(0.771) 		0.169
(0.387) 		0.373
(0.595) 		0.159
(0.375)
7q loss 37 (13%) 258 0.0982
(0.282) 		0.171
(0.389) 		0.0153
(0.096) 		0.0736
(0.238) 		0.337
(0.559) 		0.219
(0.437) 		0.145
(0.358) 		0.255
(0.482) 		0.571
(0.76) 		0.575
(0.764)
9p loss 54 (18%) 241 0.00177
(0.0217) 		0.692
(0.819) 		0.187
(0.417) 		0.481
(0.685) 		0.509
(0.708) 		0.591
(0.771) 		0.927
(0.96) 		0.952
(0.979) 		0.0515
(0.19) 		0.799
(0.884)
10p loss 66 (22%) 229 0.00037
(0.00892) 		0.412
(0.634) 		0.0583
(0.203) 		0.973
(0.989) 		0.206
(0.427) 		0.531
(0.726) 		0.711
(0.829) 		0.602
(0.771) 		0.111
(0.298) 		0.74
(0.85)
10q loss 74 (25%) 221 0.00074
(0.0135) 		0.476
(0.681) 		0.0589
(0.204) 		0.964
(0.983) 		0.0734
(0.238) 		0.251
(0.478) 		0.761
(0.864) 		0.136
(0.344) 		0.243
(0.47) 		0.557
(0.745)
12q loss 15 (5%) 280 0.363
(0.584) 		0.0435
(0.174) 		0.678
(0.815) 		0.803
(0.884) 		0.694
(0.819) 		0.41
(0.634) 		0.193
(0.418) 		0.533
(0.727) 		0.237
(0.463) 		0.909
(0.951)
15q loss 47 (16%) 248 0.0581
(0.203) 		0.895
(0.945) 		0.0218
(0.116) 		0.68
(0.815) 		0.216
(0.434) 		0.593
(0.771) 		0.297
(0.521) 		0.512
(0.71) 		0.265
(0.491) 		0.694
(0.819)
17p loss 95 (32%) 200 0.00113
(0.0172) 		0.167
(0.383) 		0.403
(0.627) 		0.58
(0.766) 		0.0571
(0.202) 		0.0551
(0.197) 		0.14
(0.35) 		0.0582
(0.203) 		0.539
(0.731) 		0.295
(0.519)
17q loss 37 (13%) 258 0.175
(0.397) 		0.0467
(0.177) 		0.485
(0.689) 		0.351
(0.573) 		0.266
(0.491) 		0.131
(0.336) 		0.0506
(0.188) 		0.334
(0.559) 		0.569
(0.758) 		0.191
(0.418)
19q loss 29 (10%) 266 0.219
(0.437) 		0.185
(0.413) 		0.426
(0.645) 		0.513
(0.71) 		0.308
(0.533) 		0.411
(0.634) 		0.269
(0.491) 		0.109
(0.298) 		0.201
(0.426) 		0.026
(0.127)
20q loss 10 (3%) 285 0.509
(0.708) 		0.21
(0.428) 		0.0338
(0.149) 		0.705
(0.827) 		0.491
(0.694) 		0.191
(0.418) 		1
(1.00) 		0.649
(0.797) 		1
(1.00) 		0.516
(0.712)
4p gain 11 (4%) 284 0.535
(0.729) 		0.861
(0.928) 		0.861
(0.928) 		0.207
(0.427) 		0.95
(0.978) 		0.595
(0.771) 		0.538
(0.73) 		0.6
(0.771) 		0.924
(0.958) 		0.875
(0.933)
4q gain 16 (5%) 279 0.324
(0.551) 		0.232
(0.454) 		0.981
(0.995) 		0.629
(0.786) 		0.592
(0.771) 		0.343
(0.565) 		0.896
(0.945) 		0.336
(0.559) 		0.899
(0.945) 		0.868
(0.931)
10p gain 25 (8%) 270 0.0758
(0.243) 		0.761
(0.864) 		0.193
(0.418) 		0.697
(0.819) 		0.817
(0.893) 		0.474
(0.68) 		0.107
(0.296) 		0.695
(0.819) 		0.864
(0.929) 		0.318
(0.546)
10q gain 17 (6%) 278 0.623
(0.785) 		0.557
(0.745) 		0.441
(0.656) 		0.696
(0.819) 		0.424
(0.645) 		0.2
(0.425) 		0.356
(0.576) 		0.916
(0.955) 		0.625
(0.786) 		0.706
(0.827)
15q gain 52 (18%) 243 0.11
(0.298) 		0.22
(0.437) 		0.812
(0.889) 		0.615
(0.78) 		0.786
(0.877) 		0.871
(0.932) 		0.733
(0.845) 		0.762
(0.864) 		0.609
(0.775) 		0.219
(0.437)
16q gain 40 (14%) 255 0.455
(0.667) 		0.32
(0.547) 		0.599
(0.771) 		0.292
(0.516) 		0.669
(0.81) 		0.432
(0.649) 		0.0938
(0.276) 		0.0869
(0.266) 		0.477
(0.682) 		0.466
(0.676)
2p loss 19 (6%) 276 0.656
(0.803) 		0.647
(0.797) 		0.557
(0.745) 		0.259
(0.487) 		0.271
(0.492) 		0.181
(0.405) 		0.521
(0.717) 		0.214
(0.434) 		0.508
(0.708) 		0.347
(0.569)
5p loss 19 (6%) 276 0.718
(0.834) 		0.459
(0.672) 		0.623
(0.785) 		0.555
(0.745) 		0.886
(0.941) 		0.734
(0.845) 		0.6
(0.771) 		0.59
(0.771) 		0.686
(0.819) 		0.11
(0.298)
'1p gain' versus 'CN_CNMF'

P value = 0.00891 (Fisher's exact test), Q value = 0.068

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
1P GAIN MUTATED 29 22 39
1P GAIN WILD-TYPE 100 51 54

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.056

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
1P GAIN MUTATED 15 22 26 12 1 14
1P GAIN WILD-TYPE 56 32 31 47 8 31

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0089

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
1P GAIN MUTATED 19 44 14 12
1P GAIN WILD-TYPE 35 56 55 57

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.017

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
1P GAIN MUTATED 12 70 7
1P GAIN WILD-TYPE 60 115 28

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0051

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
1P GAIN MUTATED 9 31 35 9 6
1P GAIN WILD-TYPE 51 64 37 16 37

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.085

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
1P GAIN MUTATED 12 22 11 39
1P GAIN WILD-TYPE 52 28 15 103

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
1Q GAIN MUTATED 46 34 60
1Q GAIN WILD-TYPE 83 39 33

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.043

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
1Q GAIN MUTATED 27 60 27 24
1Q GAIN WILD-TYPE 27 40 42 45

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00713 (Fisher's exact test), Q value = 0.058

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
1Q GAIN MUTATED 24 100 14
1Q GAIN WILD-TYPE 48 85 21

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.038

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
1Q GAIN MUTATED 19 51 42 14 14
1Q GAIN WILD-TYPE 41 44 30 11 29

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.075

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
1Q GAIN MUTATED 22 30 17 63
1Q GAIN WILD-TYPE 42 20 9 79

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
2P GAIN MUTATED 14 32 18
2P GAIN WILD-TYPE 115 41 75

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.076

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
2P GAIN MUTATED 22 10 5 16 4 7
2P GAIN WILD-TYPE 49 44 52 43 5 38

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.095

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
2P GAIN MUTATED 15 12 21 16
2P GAIN WILD-TYPE 39 88 48 53

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.17

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
2P GAIN MUTATED 21 32 11
2P GAIN WILD-TYPE 51 153 24

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.014

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
2P GAIN MUTATED 18 18 6 11 11
2P GAIN WILD-TYPE 42 77 66 14 32

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0051

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
2Q GAIN MUTATED 8 20 9
2Q GAIN WILD-TYPE 121 53 84

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.11

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
2Q GAIN MUTATED 10 5 10 12
2Q GAIN WILD-TYPE 44 95 59 57

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00449 (Fisher's exact test), Q value = 0.043

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
2Q GAIN MUTATED 13 15 9
2Q GAIN WILD-TYPE 59 170 26

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.028

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
2Q GAIN MUTATED 12 9 2 5 9
2Q GAIN WILD-TYPE 48 86 70 20 34

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00665 (Fisher's exact test), Q value = 0.056

Table S21.  Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
3P GAIN MUTATED 10 10 6 4 10
3P GAIN WILD-TYPE 22 37 39 19 7

Figure S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S22.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
3Q GAIN MUTATED 61 40 74
3Q GAIN WILD-TYPE 68 33 19

Figure S22.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0038

Table S23.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
3Q GAIN MUTATED 31 36 37 27 6 38
3Q GAIN WILD-TYPE 40 18 20 32 3 7

Figure S23.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.019

Table S24.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
3Q GAIN MUTATED 34 73 34 32
3Q GAIN WILD-TYPE 20 27 35 37

Figure S24.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0022

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
3Q GAIN MUTATED 30 128 15
3Q GAIN WILD-TYPE 42 57 20

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0068

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
3Q GAIN MUTATED 23 59 55 16 22
3Q GAIN WILD-TYPE 37 36 17 9 21

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.035

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 77 80
3Q GAIN MUTATED 60 52 55
3Q GAIN WILD-TYPE 65 25 25

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0068

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
3Q GAIN MUTATED 26 36 22 83
3Q GAIN WILD-TYPE 38 14 4 59

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S29.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
5P GAIN MUTATED 31 48 34
5P GAIN WILD-TYPE 98 25 59

Figure S29.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.11

Table S30.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
5P GAIN MUTATED 18 20 25 32 4 14
5P GAIN WILD-TYPE 53 34 32 27 5 31

Figure S30.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.15

Table S31.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
5P GAIN MUTATED 18 38 20 36
5P GAIN WILD-TYPE 36 62 49 33

Figure S31.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.095

Table S32.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
5P GAIN MUTATED 19 74 19
5P GAIN WILD-TYPE 53 111 16

Figure S32.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.15

Table S33.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
5P GAIN MUTATED 34 23 56
5P GAIN WILD-TYPE 65 54 63

Figure S33.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00839 (Fisher's exact test), Q value = 0.065

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
5P GAIN MUTATED 14 43 22 13 21
5P GAIN WILD-TYPE 46 52 50 12 22

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.13

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
5P GAIN MUTATED 16 19 7 64
5P GAIN WILD-TYPE 48 31 19 78

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00192 (Fisher's exact test), Q value = 0.023

Table S36.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
5Q GAIN MUTATED 11 20 13
5Q GAIN WILD-TYPE 118 53 80

Figure S36.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.11

Table S37.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
6P GAIN MUTATED 19 6 6 14 3 4
6P GAIN WILD-TYPE 52 48 51 45 6 41

Figure S37.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00621 (Fisher's exact test), Q value = 0.054

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
6P GAIN MUTATED 7 4 4 7 7
6P GAIN WILD-TYPE 25 43 41 16 10

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.13

Table S39.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
6P GAIN MUTATED 13 9 14 16
6P GAIN WILD-TYPE 41 91 55 53

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.16

Table S40.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
6P GAIN MUTATED 14 10 10 5 13
6P GAIN WILD-TYPE 46 85 62 20 30

Figure S40.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'RPPA_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.12

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
6Q GAIN MUTATED 3 5 3 0 2 0 2 3
6Q GAIN WILD-TYPE 23 19 17 18 29 26 4 10

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.037

Table S42.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
7P GAIN MUTATED 4 12 7 13 1 1
7P GAIN WILD-TYPE 67 42 50 46 8 44

Figure S42.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00656 (Fisher's exact test), Q value = 0.055

Table S43.  Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
7P GAIN MUTATED 2 3 2 6 0 2 2 0
7P GAIN WILD-TYPE 24 21 18 12 31 24 4 13

Figure S43.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.13

Table S44.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
7P GAIN MUTATED 4 13 5 16
7P GAIN WILD-TYPE 50 87 64 53

Figure S44.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.011

Table S45.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
7P GAIN MUTATED 9 3 26
7P GAIN WILD-TYPE 90 74 93

Figure S45.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.18

Table S46.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
7Q GAIN MUTATED 10 14 13
7Q GAIN WILD-TYPE 119 59 80

Figure S46.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.055

Table S47.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
7Q GAIN MUTATED 3 14 8 7 2 3
7Q GAIN WILD-TYPE 68 40 49 52 7 42

Figure S47.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0054 (Fisher's exact test), Q value = 0.048

Table S48.  Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
7Q GAIN MUTATED 0 2 1 6 2 2 2 0
7Q GAIN WILD-TYPE 26 22 19 12 29 24 4 13

Figure S48.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.015

Table S49.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
7Q GAIN MUTATED 9 3 25
7Q GAIN WILD-TYPE 90 74 94

Figure S49.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.076

Table S50.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 77 80
7Q GAIN MUTATED 17 3 15
7Q GAIN WILD-TYPE 108 74 65

Figure S50.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.12

Table S51.  Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
8P GAIN MUTATED 11 25 5 12
8P GAIN WILD-TYPE 43 75 64 57

Figure S51.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.13

Table S52.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
8P GAIN MUTATED 5 26 13 2 7
8P GAIN WILD-TYPE 55 69 59 23 36

Figure S52.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.13

Table S53.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
8P GAIN MUTATED 4 9 6 31
8P GAIN WILD-TYPE 60 41 20 111

Figure S53.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.076

Table S54.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
8Q GAIN MUTATED 12 22 19 19 6 13
8Q GAIN WILD-TYPE 59 32 38 40 3 32

Figure S54.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.11

Table S55.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
8Q GAIN MUTATED 19 36 11 24
8Q GAIN WILD-TYPE 35 64 58 45

Figure S55.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.019

Table S56.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
8Q GAIN MUTATED 11 70 9
8Q GAIN WILD-TYPE 61 115 26

Figure S56.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00684 (Fisher's exact test), Q value = 0.056

Table S57.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
8Q GAIN MUTATED 9 40 21 6 15
8Q GAIN WILD-TYPE 51 55 51 19 28

Figure S57.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0061

Table S58.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
8Q GAIN MUTATED 7 15 7 57
8Q GAIN WILD-TYPE 57 35 19 85

Figure S58.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.18

Table S59.  Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
9P GAIN MUTATED 5 7 14 14 2 7
9P GAIN WILD-TYPE 66 47 43 45 7 38

Figure S59.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.076

Table S60.  Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
9P GAIN MUTATED 6 32 11
9P GAIN WILD-TYPE 66 153 24

Figure S60.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.11

Table S61.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
9P GAIN MUTATED 6 15 13 1 14
9P GAIN WILD-TYPE 54 80 59 24 29

Figure S61.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.13

Table S62.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
9P GAIN MUTATED 6 8 1 32
9P GAIN WILD-TYPE 58 42 25 110

Figure S62.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0034

Table S63.  Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
9Q GAIN MUTATED 1 6 15 14 4 7
9Q GAIN WILD-TYPE 70 48 42 45 5 38

Figure S63.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.076

Table S64.  Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
9Q GAIN MUTATED 10 19 3 15
9Q GAIN WILD-TYPE 44 81 66 54

Figure S64.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.006

Table S65.  Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
9Q GAIN MUTATED 2 35 10
9Q GAIN WILD-TYPE 70 150 25

Figure S65.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.13

Table S66.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
9Q GAIN MUTATED 8 16 23
9Q GAIN WILD-TYPE 91 61 96

Figure S66.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00307 (Fisher's exact test), Q value = 0.033

Table S67.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
9Q GAIN MUTATED 2 15 14 3 13
9Q GAIN WILD-TYPE 58 80 58 22 30

Figure S67.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.012

Table S68.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
9Q GAIN MUTATED 2 9 1 32
9Q GAIN WILD-TYPE 62 41 25 110

Figure S68.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.11

Table S69.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
11P GAIN MUTATED 1 2 0 2 4
11P GAIN WILD-TYPE 59 93 72 23 39

Figure S69.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.11

Table S70.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
11Q GAIN MUTATED 3 5 0
11Q GAIN WILD-TYPE 126 68 93

Figure S70.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.18

Table S71.  Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
11Q GAIN MUTATED 1 0 3 4
11Q GAIN WILD-TYPE 53 100 66 65

Figure S71.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.022

Table S72.  Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
11Q GAIN MUTATED 3 1 4
11Q GAIN WILD-TYPE 69 184 31

Figure S72.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.12

Table S73.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
11Q GAIN MUTATED 2 1 0 1 4
11Q GAIN WILD-TYPE 58 94 72 24 39

Figure S73.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00634 (Fisher's exact test), Q value = 0.055

Table S74.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
12P GAIN MUTATED 19 13 9 11
12P GAIN WILD-TYPE 35 87 60 58

Figure S74.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.085

Table S75.  Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
12Q GAIN MUTATED 18 13 9 10
12Q GAIN WILD-TYPE 36 87 60 59

Figure S75.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.17

Table S76.  Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
13Q GAIN MUTATED 11 10 2
13Q GAIN WILD-TYPE 61 175 33

Figure S76.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00548 (Fisher's exact test), Q value = 0.048

Table S77.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
13Q GAIN MUTATED 15 5 4
13Q GAIN WILD-TYPE 84 72 115

Figure S77.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.18

Table S78.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
14Q GAIN MUTATED 13 15 19
14Q GAIN WILD-TYPE 116 58 74

Figure S78.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 0.00781 (Fisher's exact test), Q value = 0.061

Table S79.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
16P GAIN MUTATED 11 11 22
16P GAIN WILD-TYPE 118 62 71

Figure S79.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.013

Table S80.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
17P GAIN MUTATED 2 10 10
17P GAIN WILD-TYPE 127 63 83

Figure S80.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0051

Table S81.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
17P GAIN MUTATED 8 1 1 3 5 4
17P GAIN WILD-TYPE 63 53 56 56 4 41

Figure S81.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.096

Table S82.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
17Q GAIN MUTATED 11 17 14
17Q GAIN WILD-TYPE 118 56 79

Figure S82.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.069

Table S83.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
17Q GAIN MUTATED 15 5 6 5 5 6
17Q GAIN WILD-TYPE 56 49 51 54 4 39

Figure S83.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.15

Table S84.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
18P GAIN MUTATED 14 18 17
18P GAIN WILD-TYPE 115 55 76

Figure S84.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.16

Table S85.  Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
18P GAIN MUTATED 15 19 7 8
18P GAIN WILD-TYPE 39 81 62 61

Figure S85.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.019

Table S86.  Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
18Q GAIN MUTATED 12 13 1 6
18Q GAIN WILD-TYPE 42 87 68 63

Figure S86.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.1

Table S87.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
19P GAIN MUTATED 11 16 17
19P GAIN WILD-TYPE 118 57 76

Figure S87.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S88.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
19Q GAIN MUTATED 16 38 18
19Q GAIN WILD-TYPE 113 35 75

Figure S88.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.17

Table S89.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
19Q GAIN MUTATED 13 43 14
19Q GAIN WILD-TYPE 59 142 21

Figure S89.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.013

Table S90.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
20P GAIN MUTATED 29 34 37
20P GAIN WILD-TYPE 100 39 56

Figure S90.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00495 (Fisher's exact test), Q value = 0.045

Table S91.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
20P GAIN MUTATED 31 26 16 11 4 12
20P GAIN WILD-TYPE 40 28 41 48 5 33

Figure S91.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0073 (Fisher's exact test), Q value = 0.058

Table S92.  Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
20P GAIN MUTATED 10 13 16 6 13
20P GAIN WILD-TYPE 22 34 29 17 4

Figure S92.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 0.00476 (Fisher's exact test), Q value = 0.044

Table S93.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
20Q GAIN MUTATED 37 36 42
20Q GAIN WILD-TYPE 92 37 51

Figure S93.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.044

Table S94.  Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
20Q GAIN MUTATED 7 11 8 7 12 6 5 11
20Q GAIN WILD-TYPE 19 13 12 11 19 20 1 2

Figure S94.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00244 (Fisher's exact test), Q value = 0.028

Table S95.  Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
20Q GAIN MUTATED 12 13 20 8 14
20Q GAIN WILD-TYPE 20 34 25 15 3

Figure S95.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.15

Table S96.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
20Q GAIN MUTATED 30 32 23 15 15
20Q GAIN WILD-TYPE 30 63 49 10 28

Figure S96.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.1

Table S97.  Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
21Q GAIN MUTATED 9 19 6 3
21Q GAIN WILD-TYPE 45 81 63 66

Figure S97.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0061

Table S98.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
22Q GAIN MUTATED 15 5 3 6
22Q GAIN WILD-TYPE 39 95 66 63

Figure S98.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.13

Table S99.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
XP GAIN MUTATED 13 8 21
XP GAIN WILD-TYPE 116 65 72

Figure S99.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.12

Table S100.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
XQ GAIN MUTATED 11 11 20
XQ GAIN WILD-TYPE 118 62 73

Figure S100.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.15

Table S101.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
XQ GAIN MUTATED 6 12 5 9 4 6
XQ GAIN WILD-TYPE 65 42 52 50 5 39

Figure S101.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.011

Table S102.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
1P LOSS MUTATED 2 0 2 9
1P LOSS WILD-TYPE 52 100 67 60

Figure S102.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.11

Table S103.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
1P LOSS MUTATED 3 5 5
1P LOSS WILD-TYPE 69 180 30

Figure S103.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.11

Table S104.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
1Q LOSS MUTATED 2 6 1
1Q LOSS WILD-TYPE 127 67 92

Figure S104.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.17

Table S105.  Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
1Q LOSS MUTATED 1 1 1 6
1Q LOSS WILD-TYPE 53 99 68 63

Figure S105.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.07

Table S106.  Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
2Q LOSS MUTATED 3 21 4 7
2Q LOSS WILD-TYPE 51 79 65 62

Figure S106.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.048 (Fisher's exact test), Q value = 0.18

Table S107.  Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
2Q LOSS MUTATED 4 29 2
2Q LOSS WILD-TYPE 68 156 33

Figure S107.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.12

Table S108.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
2Q LOSS MUTATED 3 17 10 4 1
2Q LOSS WILD-TYPE 57 78 62 21 42

Figure S108.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0089

Table S109.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
3P LOSS MUTATED 10 22 10 21 6 13
3P LOSS WILD-TYPE 61 32 47 38 3 32

Figure S109.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.14

Table S110.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
3P LOSS MUTATED 19 31 10 21
3P LOSS WILD-TYPE 35 69 59 48

Figure S110.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.012

Table S111.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
3P LOSS MUTATED 9 65 7
3P LOSS WILD-TYPE 63 120 28

Figure S111.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.13

Table S112.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
3P LOSS MUTATED 18 24 40
3P LOSS WILD-TYPE 81 53 79

Figure S112.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0037 (Fisher's exact test), Q value = 0.038

Table S113.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
3P LOSS MUTATED 6 33 25 8 10
3P LOSS WILD-TYPE 54 62 47 17 33

Figure S113.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.027

Table S114.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 77 80
3P LOSS MUTATED 25 19 34
3P LOSS WILD-TYPE 100 58 46

Figure S114.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.016

Table S115.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
3P LOSS MUTATED 6 17 10 45
3P LOSS WILD-TYPE 58 33 16 97

Figure S115.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.16

Table S116.  Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
3Q LOSS MUTATED 3 2 0 7 1 1
3Q LOSS WILD-TYPE 68 52 57 52 8 44

Figure S116.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.13

Table S117.  Gene #47: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
3Q LOSS MUTATED 1 1 3 5 0
3Q LOSS WILD-TYPE 31 46 42 18 17

Figure S117.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.11

Table S118.  Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
3Q LOSS MUTATED 4 1 2 7
3Q LOSS WILD-TYPE 50 99 67 62

Figure S118.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S119.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
4P LOSS MUTATED 32 48 51
4P LOSS WILD-TYPE 97 25 42

Figure S119.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.044

Table S120.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
4P LOSS MUTATED 26 53 18 32
4P LOSS WILD-TYPE 28 47 51 37

Figure S120.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.022

Table S121.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
4P LOSS MUTATED 20 88 21
4P LOSS WILD-TYPE 52 97 14

Figure S121.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.014

Table S122.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
4P LOSS MUTATED 13 52 31 12 23
4P LOSS WILD-TYPE 47 43 41 13 20

Figure S122.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.011

Table S123.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
4P LOSS MUTATED 15 26 17 66
4P LOSS WILD-TYPE 49 24 9 76

Figure S123.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S124.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
4Q LOSS MUTATED 16 45 32
4Q LOSS WILD-TYPE 113 28 61

Figure S124.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.088

Table S125.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
4Q LOSS MUTATED 21 53 19
4Q LOSS WILD-TYPE 51 132 16

Figure S125.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.022

Table S126.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
5Q LOSS MUTATED 15 23 13
5Q LOSS WILD-TYPE 114 50 80

Figure S126.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.13

Table S127.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
5Q LOSS MUTATED 11 11 29
5Q LOSS WILD-TYPE 88 66 90

Figure S127.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.17

Table S128.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
5Q LOSS MUTATED 8 9 10 23
5Q LOSS WILD-TYPE 56 41 16 119

Figure S128.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.16

Table S129.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
6P LOSS MUTATED 5 15 9 11 0 7
6P LOSS WILD-TYPE 66 39 48 48 9 38

Figure S129.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.13

Table S130.  Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
6P LOSS MUTATED 5 37 5
6P LOSS WILD-TYPE 67 148 30

Figure S130.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.00468 (Fisher's exact test), Q value = 0.044

Table S131.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
6Q LOSS MUTATED 31 28 15
6Q LOSS WILD-TYPE 98 45 78

Figure S131.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00786 (Fisher's exact test), Q value = 0.061

Table S132.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
6Q LOSS MUTATED 10 22 14 19 2 7
6Q LOSS WILD-TYPE 61 32 43 40 7 38

Figure S132.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.13

Table S133.  Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
6Q LOSS MUTATED 10 54 10
6Q LOSS WILD-TYPE 62 131 25

Figure S133.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.15

Table S134.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
6Q LOSS MUTATED 8 28 17 11 10
6Q LOSS WILD-TYPE 52 67 55 14 33

Figure S134.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.18

Table S135.  Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
7P LOSS MUTATED 6 7 13
7P LOSS WILD-TYPE 123 66 80

Figure S135.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.16

Table S136.  Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
7P LOSS MUTATED 9 7 8 2
7P LOSS WILD-TYPE 45 93 61 67

Figure S136.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'RPPA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.096

Table S137.  Gene #55: '7q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
7Q LOSS MUTATED 7 8 3 1 6 0 0 1
7Q LOSS WILD-TYPE 19 16 17 17 25 26 6 12

Figure S137.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0051

Table S138.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
8P LOSS MUTATED 23 34 25
8P LOSS WILD-TYPE 106 39 68

Figure S138.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.11

Table S139.  Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
8P LOSS MUTATED 17 19 18 28
8P LOSS WILD-TYPE 37 81 51 41

Figure S139.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.11

Table S140.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
8P LOSS MUTATED 27 13 42
8P LOSS WILD-TYPE 72 64 77

Figure S140.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.18

Table S141.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
8P LOSS MUTATED 19 22 14 8 19
8P LOSS WILD-TYPE 41 73 58 17 24

Figure S141.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.076

Table S142.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 77 80
8P LOSS MUTATED 36 14 32
8P LOSS WILD-TYPE 89 63 48

Figure S142.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0051

Table S143.  Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
8Q LOSS MUTATED 14 0 1 8 0 1
8Q LOSS WILD-TYPE 57 54 56 51 9 44

Figure S143.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.17

Table S144.  Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
8Q LOSS MUTATED 0 7 2 3 3
8Q LOSS WILD-TYPE 32 40 43 20 14

Figure S144.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0051

Table S145.  Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
8Q LOSS MUTATED 6 0 10 8
8Q LOSS WILD-TYPE 48 100 59 61

Figure S145.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0038

Table S146.  Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
8Q LOSS MUTATED 14 6 4
8Q LOSS WILD-TYPE 58 179 31

Figure S146.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.1

Table S147.  Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
8Q LOSS MUTATED 14 2 8
8Q LOSS WILD-TYPE 85 75 111

Figure S147.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0064

Table S148.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
8Q LOSS MUTATED 12 3 1 2 6
8Q LOSS WILD-TYPE 48 92 71 23 37

Figure S148.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00148 (Fisher's exact test), Q value = 0.02

Table S149.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
8Q LOSS MUTATED 12 0 3 9
8Q LOSS WILD-TYPE 52 50 23 133

Figure S149.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.022

Table S150.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
9P LOSS MUTATED 14 23 17
9P LOSS WILD-TYPE 115 50 76

Figure S150.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0061

Table S151.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
9Q LOSS MUTATED 11 23 17
9Q LOSS WILD-TYPE 118 50 76

Figure S151.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.17

Table S152.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
9Q LOSS MUTATED 20 10 4 9 2 6
9Q LOSS WILD-TYPE 51 44 53 50 7 39

Figure S152.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.022

Table S153.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 77 80
9Q LOSS MUTATED 32 10 6
9Q LOSS WILD-TYPE 93 67 74

Figure S153.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0089

Table S154.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
10P LOSS MUTATED 22 29 15
10P LOSS WILD-TYPE 107 44 78

Figure S154.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.013

Table S155.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
10Q LOSS MUTATED 25 31 18
10Q LOSS WILD-TYPE 104 42 75

Figure S155.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.02

Table S156.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
11P LOSS MUTATED 30 34 36
11P LOSS WILD-TYPE 99 39 57

Figure S156.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.13

Table S157.  Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
11P LOSS MUTATED 5 9 16 8 9
11P LOSS WILD-TYPE 27 38 29 15 8

Figure S157.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.14

Table S158.  Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
11P LOSS MUTATED 23 38 14 25
11P LOSS WILD-TYPE 31 62 55 44

Figure S158.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.002

Table S159.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
11Q LOSS MUTATED 33 28 54
11Q LOSS WILD-TYPE 96 45 39

Figure S159.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.15

Table S160.  Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
11Q LOSS MUTATED 27 45 20 22
11Q LOSS WILD-TYPE 27 55 49 47

Figure S160.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00727 (Fisher's exact test), Q value = 0.058

Table S161.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
11Q LOSS MUTATED 17 50 29 8 11
11Q LOSS WILD-TYPE 43 45 43 17 32

Figure S161.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.12

Table S162.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
12P LOSS MUTATED 12 17 11
12P LOSS WILD-TYPE 117 56 82

Figure S162.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.093

Table S163.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
12P LOSS MUTATED 10 14 2 8 2 4
12P LOSS WILD-TYPE 61 40 55 51 7 41

Figure S163.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0079

Table S164.  Gene #64: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
12P LOSS MUTATED 3 8 4 3 0 1 3 0
12P LOSS WILD-TYPE 23 16 16 15 31 25 3 13

Figure S164.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.013

Table S165.  Gene #64: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
12P LOSS MUTATED 2 4 6 10 0
12P LOSS WILD-TYPE 30 43 39 13 17

Figure S165.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.17

Table S166.  Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
12Q LOSS MUTATED 4 5 0 2 2 2
12Q LOSS WILD-TYPE 67 49 57 57 7 43

Figure S166.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.016

Table S167.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
13Q LOSS MUTATED 23 31 26
13Q LOSS WILD-TYPE 106 42 67

Figure S167.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.14

Table S168.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
13Q LOSS MUTATED 12 18 17 20 5 8
13Q LOSS WILD-TYPE 59 36 40 39 4 37

Figure S168.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.11

Table S169.  Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
13Q LOSS MUTATED 19 25 10 24
13Q LOSS WILD-TYPE 35 75 59 45

Figure S169.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.18

Table S170.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
13Q LOSS MUTATED 12 53 13
13Q LOSS WILD-TYPE 60 132 22

Figure S170.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.036

Table S171.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
13Q LOSS MUTATED 7 29 17 12 15
13Q LOSS WILD-TYPE 53 66 55 13 28

Figure S171.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.016

Table S172.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
14Q LOSS MUTATED 11 18 6
14Q LOSS WILD-TYPE 118 55 87

Figure S172.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.096

Table S173.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 77 80
14Q LOSS MUTATED 23 6 5
14Q LOSS WILD-TYPE 102 71 75

Figure S173.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.12

Table S174.  Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
15Q LOSS MUTATED 5 5 0 4 3 1 3 1
15Q LOSS WILD-TYPE 21 19 20 14 28 25 3 12

Figure S174.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.14

Table S175.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
16P LOSS MUTATED 12 4 2 9 3 4
16P LOSS WILD-TYPE 59 50 55 50 6 41

Figure S175.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.13

Table S176.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
16P LOSS MUTATED 11 5 9 9
16P LOSS WILD-TYPE 43 95 60 60

Figure S176.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00997 (Fisher's exact test), Q value = 0.074

Table S177.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
16P LOSS MUTATED 8 10 2 6 8
16P LOSS WILD-TYPE 52 85 70 19 35

Figure S177.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.038

Table S178.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
16Q LOSS MUTATED 20 6 3 7 3 5
16Q LOSS WILD-TYPE 51 48 54 52 6 40

Figure S178.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.12

Table S179.  Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
16Q LOSS MUTATED 3 5 1 5 9 0 1 3
16Q LOSS WILD-TYPE 23 19 19 13 22 26 5 10

Figure S179.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.022

Table S180.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
16Q LOSS MUTATED 11 8 19 6
16Q LOSS WILD-TYPE 43 92 50 63

Figure S180.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.017

Table S181.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
16Q LOSS MUTATED 21 20 3
16Q LOSS WILD-TYPE 51 165 32

Figure S181.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0094 (Fisher's exact test), Q value = 0.07

Table S182.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
16Q LOSS MUTATED 23 11 10
16Q LOSS WILD-TYPE 76 66 109

Figure S182.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.017

Table S183.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
16Q LOSS MUTATED 17 12 3 6 6
16Q LOSS WILD-TYPE 43 83 69 19 37

Figure S183.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.093

Table S184.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
16Q LOSS MUTATED 18 4 4 17
16Q LOSS WILD-TYPE 46 46 22 125

Figure S184.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.017

Table S185.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
17P LOSS MUTATED 28 33 34
17P LOSS WILD-TYPE 101 40 59

Figure S185.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.18

Table S186.  Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
17Q LOSS MUTATED 5 13 4 10 1 4
17Q LOSS WILD-TYPE 66 41 53 49 8 41

Figure S186.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.076

Table S187.  Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
18P LOSS MUTATED 7 11 19 18
18P LOSS WILD-TYPE 47 89 50 51

Figure S187.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.16

Table S188.  Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
18P LOSS MUTATED 20 27 8
18P LOSS WILD-TYPE 52 158 27

Figure S188.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0347 (Fisher's exact test), Q value = 0.15

Table S189.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
18P LOSS MUTATED 19 12 10 4 10
18P LOSS WILD-TYPE 41 83 62 21 33

Figure S189.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.013

Table S190.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
18Q LOSS MUTATED 27 8 8 22 2 6
18Q LOSS WILD-TYPE 44 46 49 37 7 39

Figure S190.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0022

Table S191.  Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
18Q LOSS MUTATED 13 9 26 25
18Q LOSS WILD-TYPE 41 91 43 44

Figure S191.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.016

Table S192.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
18Q LOSS MUTATED 27 33 13
18Q LOSS WILD-TYPE 45 152 22

Figure S192.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0061

Table S193.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
18Q LOSS MUTATED 25 15 11 5 17
18Q LOSS WILD-TYPE 35 80 61 20 26

Figure S193.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.11

Table S194.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
18Q LOSS MUTATED 24 6 6 37
18Q LOSS WILD-TYPE 40 44 20 105

Figure S194.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.002

Table S195.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
19P LOSS MUTATED 14 31 15
19P LOSS WILD-TYPE 115 42 78

Figure S195.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.011

Table S196.  Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
19P LOSS MUTATED 18 8 3 22 2 7
19P LOSS WILD-TYPE 53 46 54 37 7 38

Figure S196.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.02

Table S197.  Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
19P LOSS MUTATED 13 9 16 22
19P LOSS WILD-TYPE 41 91 53 47

Figure S197.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.029

Table S198.  Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
19P LOSS MUTATED 18 28 14
19P LOSS WILD-TYPE 54 157 21

Figure S198.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.13

Table S199.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
19P LOSS MUTATED 25 8 27
19P LOSS WILD-TYPE 74 69 92

Figure S199.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0061

Table S200.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
19P LOSS MUTATED 13 15 6 12 14
19P LOSS WILD-TYPE 47 80 66 13 29

Figure S200.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.18

Table S201.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 77 80
19P LOSS MUTATED 29 9 21
19P LOSS WILD-TYPE 96 68 59

Figure S201.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.096

Table S202.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
19P LOSS MUTATED 14 3 8 34
19P LOSS WILD-TYPE 50 47 18 108

Figure S202.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.13

Table S203.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 50 26 142
19Q LOSS MUTATED 8 1 6 14
19Q LOSS WILD-TYPE 56 49 20 128

Figure S203.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'RPPA_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.092

Table S204.  Gene #77: '20p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
20P LOSS MUTATED 0 1 0 2 2 0 2 2
20P LOSS WILD-TYPE 26 23 20 16 29 26 4 11

Figure S204.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.12

Table S205.  Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
20P LOSS MUTATED 1 5 6 11
20P LOSS WILD-TYPE 53 95 63 58

Figure S205.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q loss' versus 'RPPA_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.15

Table S206.  Gene #78: '20q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 26 24 20 18 31 26 6 13
20Q LOSS MUTATED 0 0 0 2 0 0 0 1
20Q LOSS WILD-TYPE 26 24 20 16 31 26 6 12

Figure S206.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0022

Table S207.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
21Q LOSS MUTATED 9 24 16
21Q LOSS WILD-TYPE 120 49 77

Figure S207.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.18

Table S208.  Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
21Q LOSS MUTATED 13 4 7 17 2 6
21Q LOSS WILD-TYPE 58 50 50 42 7 39

Figure S208.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.13

Table S209.  Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
21Q LOSS MUTATED 6 5 2 4 6
21Q LOSS WILD-TYPE 26 42 43 19 11

Figure S209.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.11

Table S210.  Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 100 69 69
21Q LOSS MUTATED 13 9 10 17
21Q LOSS WILD-TYPE 41 91 59 52

Figure S210.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00398 (Fisher's exact test), Q value = 0.039

Table S211.  Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
21Q LOSS MUTATED 12 24 13
21Q LOSS WILD-TYPE 60 161 22

Figure S211.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.13

Table S212.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
21Q LOSS MUTATED 8 13 8 9 11
21Q LOSS WILD-TYPE 52 82 64 16 32

Figure S212.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.027

Table S213.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
22Q LOSS MUTATED 21 28 22
22Q LOSS WILD-TYPE 108 45 71

Figure S213.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.11

Table S214.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
22Q LOSS MUTATED 21 36 14
22Q LOSS WILD-TYPE 51 149 21

Figure S214.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.043

Table S215.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
XP LOSS MUTATED 22 26 15
XP LOSS WILD-TYPE 107 47 78

Figure S215.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.029

Table S216.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 54 57 59 9 45
XP LOSS MUTATED 13 16 4 20 3 7
XP LOSS WILD-TYPE 58 38 53 39 6 38

Figure S216.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.13

Table S217.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 77 119
XP LOSS MUTATED 21 9 33
XP LOSS WILD-TYPE 78 68 86

Figure S217.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.11

Table S218.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 77 80
XP LOSS MUTATED 26 10 25
XP LOSS WILD-TYPE 99 67 55

Figure S218.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.18

Table S219.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 73 93
XQ LOSS MUTATED 23 22 14
XQ LOSS WILD-TYPE 106 51 79

Figure S219.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.13

Table S220.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 77 80
XQ LOSS MUTATED 25 9 23
XQ LOSS WILD-TYPE 100 68 57

Figure S220.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/19779738/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/20124378/CESC-TP.transferedmergedcluster.txt

  • Number of patients = 295

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • 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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