Correlation between copy number variations of arm-level result and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1JW8D00
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/C1JW8D00
Overview
Introduction

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

Summary

Testing the association between copy number variation 69 arm-level events and 10 molecular subtypes across 162 patients, 139 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'METHLYATION_CNMF'.

  • 5q gain cnv correlated to 'METHLYATION_CNMF'.

  • 6q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 15q gain cnv correlated to 'METHLYATION_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'METHLYATION_CNMF'.

  • 20q gain cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • 1q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 2p loss cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 4q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 5p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 8q loss cnv correlated to 'CN_CNMF'.

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

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 14q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'METHLYATION_CNMF'.

  • 16q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 69 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 139 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
1p loss 98 (60%) 64 1e-05
(0.00115) 		0.0152
(0.123) 		0.00562
(0.0636) 		0.00012
(0.0046) 		0.00291
(0.0372) 		0.00183
(0.0269) 		6e-05
(0.00244) 		0.0136
(0.114) 		0.00057
(0.0119) 		0.137
(0.439)
6q loss 19 (12%) 143 0.00097
(0.0167) 		0.00049
(0.0117) 		0.0202
(0.141) 		0.116
(0.399) 		0.00049
(0.0117) 		5e-05
(0.00244) 		0.00033
(0.00843) 		2e-05
(0.00138) 		0.0124
(0.111) 		0.00237
(0.0321)
11p loss 54 (33%) 108 1e-05
(0.00115) 		0.00056
(0.0119) 		0.00115
(0.0194) 		0.14
(0.444) 		0.00025
(0.00747) 		1e-05
(0.00115) 		3e-05
(0.00172) 		2e-05
(0.00138) 		5e-05
(0.00244) 		0.00247
(0.0328)
3p loss 62 (38%) 100 0.00061
(0.0124) 		0.0953
(0.35) 		0.0034
(0.0421) 		0.258
(0.584) 		0.00032
(0.00843) 		1e-05
(0.00115) 		0.00089
(0.0162) 		0.00121
(0.0199) 		0.00025
(0.00747) 		0.00018
(0.00654)
3q loss 88 (54%) 74 6e-05
(0.00244) 		0.521
(0.777) 		0.0565
(0.262) 		0.0261
(0.164) 		0.0429
(0.219) 		1e-05
(0.00115) 		0.00354
(0.0429) 		0.0304
(0.18) 		0.0119
(0.108) 		0.016
(0.127)
11q loss 40 (25%) 122 2e-05
(0.00138) 		0.0693
(0.297) 		0.0231
(0.152) 		0.116
(0.399) 		0.00026
(0.00747) 		0.00073
(0.0144) 		0.00019
(0.00655) 		0.00031
(0.00843) 		0.0002
(0.00657) 		0.0262
(0.164)
22q loss 58 (36%) 104 1e-05
(0.00115) 		0.0127
(0.111) 		0.365
(0.681) 		0.0842
(0.324) 		0.0322
(0.184) 		0.00207
(0.0291) 		0.0476
(0.238) 		0.0515
(0.252) 		0.0269
(0.167) 		0.0244
(0.157)
xp loss 48 (30%) 114 2e-05
(0.00138) 		0.00181
(0.0269) 		0.0584
(0.267) 		0.441
(0.741) 		0.0129
(0.112) 		0.00096
(0.0167) 		0.00254
(0.0331) 		0.0178
(0.135) 		0.24
(0.563) 		0.0182
(0.135)
xq loss 49 (30%) 113 3e-05
(0.00172) 		0.0014
(0.0225) 		0.0724
(0.298) 		0.612
(0.834) 		0.00735
(0.076) 		0.00055
(0.0119) 		0.00375
(0.0446) 		0.0104
(0.0968) 		0.212
(0.544) 		0.0133
(0.113)
13q gain 9 (6%) 153 0.0186
(0.136) 		0.0214
(0.146) 		0.243
(0.565) 		0.623
(0.836) 		0.00974
(0.0921) 		0.0094
(0.0914) 		0.024
(0.156) 		0.0535
(0.257) 		0.00964
(0.0921) 		0.36
(0.678)
17p loss 61 (38%) 101 0.00051
(0.0117) 		0.00236
(0.0321) 		0.492
(0.763) 		0.159
(0.456) 		0.0714
(0.298) 		0.0334
(0.188) 		0.0229
(0.152) 		0.0222
(0.149) 		0.214
(0.546) 		0.0139
(0.115)
xp gain 6 (4%) 156 0.152
(0.449) 		0.018
(0.135) 		0.035
(0.195) 		0.0168
(0.132) 		0.157
(0.454) 		0.0697
(0.297) 		0.0202
(0.141) 		0.299
(0.636)
7q loss 6 (4%) 156 0.0322
(0.184) 		0.48
(0.762) 		0.0404
(0.211) 		0.174
(0.486) 		0.0298
(0.18) 		0.0248
(0.159) 		0.247
(0.572) 		0.129
(0.421)
7q gain 22 (14%) 140 0.00743
(0.076) 		0.00628
(0.0688) 		0.448
(0.741) 		0.0187
(0.136) 		0.172
(0.484) 		0.284
(0.628) 		0.143
(0.444) 		0.114
(0.398) 		0.522
(0.777) 		0.46
(0.744)
12p gain 11 (7%) 151 0.011
(0.101) 		0.00737
(0.076) 		0.496
(0.763) 		0.119
(0.402) 		0.337
(0.662) 		0.324
(0.653) 		0.0192
(0.137) 		0.216
(0.547) 		0.131
(0.427) 		0.429
(0.736)
20q gain 10 (6%) 152 0.542
(0.784) 		0.167
(0.475) 		0.485
(0.763) 		1
(1.00) 		0.0302
(0.18) 		0.062
(0.277) 		0.0391
(0.206) 		0.077
(0.304) 		0.0391
(0.206) 		0.514
(0.775)
2p loss 10 (6%) 152 0.382
(0.691) 		0.0751
(0.3) 		0.747
(0.927) 		0.426
(0.736) 		0.00464
(0.0543) 		0.18
(0.493) 		0.195
(0.52) 		0.00075
(0.0144) 		0.147
(0.449) 		0.00749
(0.076)
14q loss 20 (12%) 142 0.237
(0.563) 		0.0532
(0.257) 		0.168
(0.475) 		0.204
(0.536) 		0.31
(0.638) 		0.793
(0.953) 		0.155
(0.452) 		0.00198
(0.0285) 		0.029
(0.177) 		0.00157
(0.0246)
6q gain 8 (5%) 154 0.148
(0.449) 		0.00177
(0.0269) 		0.0367
(0.198) 		0.111
(0.392) 		0.129
(0.421) 		0.183
(0.495) 		0.0809
(0.317) 		0.267
(0.599)
xq gain 5 (3%) 157 0.177
(0.493) 		0.0447
(0.225) 		0.0528
(0.256) 		0.0545
(0.258) 		0.142
(0.444) 		0.0679
(0.296) 		0.0305
(0.18) 		0.0966
(0.353)
4p loss 11 (7%) 151 0.00342
(0.0421) 		0.146
(0.449) 		0.47
(0.75) 		0.35
(0.666) 		0.0068
(0.0733) 		0.184
(0.495) 		0.293
(0.631) 		0.391
(0.699) 		0.058
(0.267) 		0.146
(0.449)
5p loss 5 (3%) 157 0.0644
(0.285) 		0.376
(0.688) 		0.0363
(0.197) 		0.0362
(0.197) 		0.141
(0.444) 		0.168
(0.475) 		0.168
(0.475) 		0.0546
(0.258)
9p loss 11 (7%) 151 0.0492
(0.244) 		0.718
(0.915) 		0.0845
(0.324) 		0.0175
(0.134) 		0.182
(0.495) 		0.181
(0.493) 		0.672
(0.877) 		0.0686
(0.296) 		0.548
(0.789) 		0.311
(0.638)
13q loss 8 (5%) 154 0.0361
(0.197) 		0.447
(0.741) 		0.0125
(0.111) 		0.671
(0.877) 		0.312
(0.638) 		0.116
(0.399) 		0.528
(0.778) 		0.226
(0.563) 		0.549
(0.789) 		0.463
(0.744)
17q loss 19 (12%) 143 6e-05
(0.00244) 		0.903
(1.00) 		0.156
(0.454) 		0.0323
(0.184) 		0.297
(0.635) 		0.23
(0.563) 		0.37
(0.681) 		0.0879
(0.331) 		0.882
(1.00) 		0.261
(0.59)
1q gain 19 (12%) 143 0.00086
(0.016) 		0.354
(0.671) 		0.913
(1.00) 		1
(1.00) 		0.49
(0.763) 		0.594
(0.822) 		0.907
(1.00) 		0.664
(0.872) 		0.487
(0.763) 		0.847
(0.977)
2p gain 6 (4%) 156 0.507
(0.774) 		0.00573
(0.0638) 		0.748
(0.927) 		1
(1.00) 		0.24
(0.563) 		0.347
(0.666) 		0.135
(0.437) 		0.335
(0.662) 		0.191
(0.512) 		0.462
(0.744)
5q gain 7 (4%) 155 0.896
(1.00) 		0.00527
(0.0606) 		0.0731
(0.298) 		0.297
(0.635) 		0.484
(0.763) 		0.38
(0.691) 		0.941
(1.00) 		0.286
(0.63)
7p gain 27 (17%) 135 0.0212
(0.146) 		0.0738
(0.298) 		0.533
(0.78) 		0.149
(0.449) 		0.139
(0.443) 		0.381
(0.691) 		0.239
(0.563) 		0.0726
(0.298) 		0.316
(0.64) 		0.0884
(0.331)
8p gain 10 (6%) 152 0.019
(0.137) 		0.369
(0.681) 		0.816
(0.965) 		1
(1.00) 		0.0869
(0.331) 		0.091
(0.336) 		0.071
(0.298) 		0.155
(0.452) 		0.454
(0.744) 		0.1
(0.361)
15q gain 14 (9%) 148 0.25
(0.576) 		0.0326
(0.184) 		0.837
(0.971) 		0.35
(0.666) 		0.314
(0.64) 		0.77
(0.944) 		0.427
(0.736) 		0.792
(0.953) 		0.557
(0.79) 		0.925
(1.00)
16q gain 6 (4%) 156 0.0145
(0.119) 		1
(1.00) 		0.27
(0.603) 		0.701
(0.902) 		1
(1.00) 		0.768
(0.944) 		0.397
(0.707) 		0.428
(0.736)
18q gain 10 (6%) 152 0.347
(0.666) 		0.583
(0.816) 		1
(1.00) 		0.0386
(0.206) 		0.365
(0.681) 		0.534
(0.78) 		0.845
(0.977) 		0.439
(0.741) 		0.196
(0.52) 		0.532
(0.78)
19p gain 20 (12%) 142 0.0154
(0.123) 		0.0769
(0.304) 		0.408
(0.719) 		0.781
(0.952) 		0.749
(0.927) 		0.644
(0.859) 		0.275
(0.611) 		0.926
(1.00) 		0.21
(0.543) 		0.727
(0.922)
19q gain 14 (9%) 148 0.152
(0.449) 		0.0085
(0.0838) 		0.443
(0.741) 		0.539
(0.784) 		0.376
(0.688) 		0.228
(0.563) 		0.459
(0.744) 		0.667
(0.873) 		0.523
(0.777) 		0.489
(0.763)
1q loss 27 (17%) 135 0.895
(1.00) 		0.309
(0.638) 		0.908
(1.00) 		0.148
(0.449) 		0.124
(0.412) 		0.518
(0.775) 		0.663
(0.871) 		0.264
(0.593) 		0.0313
(0.183) 		0.239
(0.563)
4q loss 10 (6%) 152 0.0729
(0.298) 		0.241
(0.563) 		0.472
(0.75) 		0.35
(0.666) 		0.0175
(0.134) 		0.338
(0.663) 		0.417
(0.728) 		0.525
(0.777) 		0.327
(0.657) 		0.323
(0.653)
8p loss 20 (12%) 142 0.0216
(0.146) 		0.391
(0.699) 		0.445
(0.741) 		0.815
(0.965) 		0.124
(0.412) 		0.108
(0.383) 		0.715
(0.915) 		0.952
(1.00) 		0.28
(0.621) 		0.488
(0.763)
8q loss 12 (7%) 150 0.0434
(0.22) 		0.739
(0.927) 		0.151
(0.449) 		1
(1.00) 		0.33
(0.66) 		0.62
(0.836) 		0.111
(0.392) 		0.437
(0.741) 		0.928
(1.00) 		0.427
(0.736)
9q loss 11 (7%) 151 0.00786
(0.0786) 		0.61
(0.834) 		0.456
(0.744) 		0.349
(0.666) 		0.511
(0.775) 		0.627
(0.84) 		0.725
(0.921) 		0.401
(0.712) 		0.828
(0.971) 		0.441
(0.741)
16p loss 9 (6%) 153 0.335
(0.662) 		0.0426
(0.219) 		0.677
(0.877) 		0.445
(0.741) 		0.554
(0.79) 		0.361
(0.679) 		0.249
(0.575) 		0.403
(0.714) 		0.678
(0.877) 		0.771
(0.944)
16q loss 5 (3%) 157 0.739
(0.927) 		0.445
(0.741) 		0.746
(0.927) 		0.786
(0.953) 		0.446
(0.741) 		0.0276
(0.17) 		0.21
(0.543) 		0.59
(0.821) 		0.0905
(0.336) 		0.829
(0.971)
21q loss 36 (22%) 126 0.206
(0.54) 		0.0506
(0.249) 		0.31
(0.638) 		0.455
(0.744) 		0.0414
(0.215) 		0.939
(1.00) 		0.561
(0.791) 		0.603
(0.827) 		0.908
(1.00) 		0.717
(0.915)
1p gain 7 (4%) 155 0.119
(0.402) 		0.785
(0.953) 		0.673
(0.877) 		0.822
(0.968) 		0.895
(1.00) 		0.526
(0.777) 		0.835
(0.971) 		0.656
(0.866)
4p gain 4 (2%) 158 0.676
(0.877) 		0.367
(0.681) 		0.819
(0.968) 		0.552
(0.79) 		0.451
(0.743) 		0.789
(0.953) 		0.77
(0.944) 		1
(1.00)
4q gain 3 (2%) 159 0.0622
(0.277) 		0.803
(0.961) 		0.472
(0.75) 		0.739
(0.927) 		0.615
(0.835) 		0.836
(0.971) 		0.814
(0.965) 		0.463
(0.744)
5p gain 11 (7%) 151 0.62
(0.836) 		0.434
(0.741) 		0.602
(0.827) 		1
(1.00) 		0.916
(1.00) 		0.66
(0.869) 		0.854
(0.98) 		0.614
(0.835) 		0.83
(0.971) 		0.214
(0.546)
6p gain 15 (9%) 147 0.887
(1.00) 		0.257
(0.583) 		0.1
(0.361) 		0.201
(0.53) 		0.308
(0.638) 		0.37
(0.681) 		0.238
(0.563) 		0.305
(0.638) 		0.561
(0.791) 		0.51
(0.775)
8q gain 13 (8%) 149 0.241
(0.563) 		0.751
(0.929) 		0.598
(0.825) 		1
(1.00) 		0.0823
(0.319) 		0.075
(0.3) 		0.114
(0.398) 		0.201
(0.53) 		0.804
(0.961) 		0.0907
(0.336)
9p gain 4 (2%) 158 0.231
(0.563) 		0.0704
(0.298) 		0.152
(0.449) 		0.225
(0.563) 		0.29
(0.631) 		0.254
(0.579) 		0.303
(0.638) 		0.511
(0.775)
9q gain 3 (2%) 159 0.46
(0.744) 		0.139
(0.443) 		0.24
(0.563) 		0.239
(0.563) 		0.462
(0.744) 		0.346
(0.666) 		0.293
(0.631) 		0.557
(0.79)
10p gain 12 (7%) 150 0.513
(0.775) 		0.0733
(0.298) 		0.719
(0.915) 		0.118
(0.402) 		0.517
(0.775) 		0.517
(0.775) 		1
(1.00) 		0.842
(0.975) 		0.489
(0.763) 		0.179
(0.493)
10q gain 10 (6%) 152 0.103
(0.369) 		0.693
(0.894) 		0.718
(0.915) 		0.12
(0.403) 		0.492
(0.763) 		0.592
(0.821) 		0.705
(0.906) 		0.507
(0.774) 		0.426
(0.736) 		0.154
(0.452)
11p gain 5 (3%) 157 0.0875
(0.331) 		0.514
(0.775) 		0.831
(0.971) 		1
(1.00) 		0.412
(0.723) 		0.305
(0.638) 		0.539
(0.784) 		0.494
(0.763) 		0.345
(0.666) 		0.69
(0.892)
12q gain 14 (9%) 148 0.0686
(0.296) 		0.225
(0.563) 		0.851
(0.98) 		0.49
(0.763) 		0.603
(0.827) 		0.653
(0.865) 		0.0612
(0.277) 		0.291
(0.631) 		0.223
(0.561) 		0.436
(0.741)
14q gain 4 (2%) 158 0.0618
(0.277) 		0.368
(0.681) 		0.551
(0.79) 		0.554
(0.79) 		0.287
(0.63) 		0.789
(0.953) 		0.769
(0.944) 		0.872
(0.994)
16p gain 6 (4%) 156 0.239
(0.563) 		0.557
(0.79) 		0.744
(0.927) 		0.74
(0.927) 		0.384
(0.692) 		0.815
(0.965) 		0.292
(0.631) 		0.502
(0.771)
17q gain 5 (3%) 157 0.545
(0.786) 		0.312
(0.638) 		0.22
(0.555) 		0.337
(0.662) 		0.3
(0.636) 		0.304
(0.638) 		0.541
(0.784) 		0.774
(0.945) 		0.541
(0.784) 		0.212
(0.544)
18p gain 8 (5%) 154 0.149
(0.449) 		0.23
(0.563) 		1
(1.00) 		0.119
(0.402) 		0.383
(0.691) 		0.651
(0.864) 		0.465
(0.745) 		0.561
(0.791) 		0.129
(0.421) 		0.855
(0.98)
20p gain 12 (7%) 150 0.646
(0.859) 		0.367
(0.681) 		0.623
(0.836) 		0.729
(0.922) 		0.18
(0.493) 		0.343
(0.666) 		0.169
(0.475) 		0.383
(0.691) 		0.593
(0.821) 		0.59
(0.821)
21q gain 3 (2%) 159 0.251
(0.576) 		0.136
(0.439) 		0.238
(0.563) 		0.0682
(0.296) 		0.184
(0.495) 		0.409
(0.719) 		0.291
(0.631) 		0.806
(0.961)
22q gain 3 (2%) 159 0.252
(0.577) 		0.0817
(0.318) 		0.238
(0.563) 		0.15
(0.449) 		0.18
(0.493) 		0.408
(0.719) 		0.0563
(0.262) 		0.807
(0.961)
2q loss 13 (8%) 149 0.822
(0.968) 		0.45
(0.742) 		0.748
(0.927) 		0.427
(0.736) 		0.417
(0.728) 		0.143
(0.444) 		0.53
(0.78) 		0.0976
(0.355) 		0.328
(0.657) 		0.34
(0.665)
5q loss 7 (4%) 155 0.386
(0.693) 		0.785
(0.953) 		0.494
(0.763) 		1
(1.00) 		0.646
(0.859) 		0.524
(0.777) 		0.896
(1.00) 		0.358
(0.677) 		0.227
(0.563) 		0.304
(0.638)
15q loss 3 (2%) 159 0.348
(0.666) 		0.333
(0.661) 		1
(1.00) 		0.866
(0.99) 		0.617
(0.836) 		0.836
(0.971) 		0.9
(1.00) 		1
(1.00)
18p loss 16 (10%) 146 0.503
(0.771) 		0.744
(0.927) 		0.435
(0.741) 		0.208
(0.542) 		0.855
(0.98) 		0.758
(0.935) 		0.893
(1.00) 		0.312
(0.638) 		0.607
(0.831) 		0.455
(0.744)
18q loss 6 (4%) 156 0.288
(0.63) 		0.874
(0.995) 		0.833
(0.971) 		0.055
(0.258) 		0.584
(0.816) 		0.656
(0.866) 		0.573
(0.805) 		0.583
(0.816) 		0.432
(0.74) 		0.867
(0.99)
19q loss 6 (4%) 156 0.242
(0.563) 		1
(1.00) 		0.942
(1.00) 		0.943
(1.00) 		0.332
(0.661) 		0.623
(0.836) 		0.927
(1.00) 		0.932
(1.00)
20q loss 3 (2%) 159 1
(1.00) 		1
(1.00) 		1
(1.00) 		0.643
(0.859) 		0.79
(0.953) 		1
(1.00) 		0.73
(0.922) 		0.806
(0.961)
'1q gain' versus 'CN_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
1Q GAIN MUTATED 6 2 11
1Q GAIN WILD-TYPE 54 61 28

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.064

Table S2.  Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
2P GAIN MUTATED 5 1 0
2P GAIN WILD-TYPE 35 77 44

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00527 (Fisher's exact test), Q value = 0.061

Table S3.  Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
5Q GAIN MUTATED 2 0 5
5Q GAIN WILD-TYPE 38 78 39

Figure S3.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.027

Table S4.  Gene #9: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
6Q GAIN MUTATED 2 0 6
6Q GAIN WILD-TYPE 38 78 38

Figure S4.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.2

Table S5.  Gene #9: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
6Q GAIN MUTATED 1 1 6 0
6Q GAIN WILD-TYPE 32 63 38 21

Figure S5.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.15

Table S6.  Gene #10: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
7P GAIN MUTATED 4 15 8
7P GAIN WILD-TYPE 56 48 31

Figure S6.  Get High-res Image Gene #10: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 0.00743 (Fisher's exact test), Q value = 0.076

Table S7.  Gene #11: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
7Q GAIN MUTATED 2 13 7
7Q GAIN WILD-TYPE 58 50 32

Figure S7.  Get High-res Image Gene #11: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00628 (Fisher's exact test), Q value = 0.069

Table S8.  Gene #11: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
7Q GAIN MUTATED 8 4 10
7Q GAIN WILD-TYPE 32 74 34

Figure S8.  Get High-res Image Gene #11: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.14

Table S9.  Gene #11: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
7Q GAIN MUTATED 1 2 8
7Q GAIN WILD-TYPE 30 16 20

Figure S9.  Get High-res Image Gene #11: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.14

Table S10.  Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
8P GAIN MUTATED 0 6 4
8P GAIN WILD-TYPE 60 57 35

Figure S10.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.1

Table S11.  Gene #19: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
12P GAIN MUTATED 1 3 7
12P GAIN WILD-TYPE 59 60 32

Figure S11.  Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00737 (Fisher's exact test), Q value = 0.076

Table S12.  Gene #19: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
12P GAIN MUTATED 4 1 6
12P GAIN WILD-TYPE 36 77 38

Figure S12.  Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.14

Table S13.  Gene #19: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
12P GAIN MUTATED 9 1 1
12P GAIN WILD-TYPE 56 57 38

Figure S13.  Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.14

Table S14.  Gene #21: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
13Q GAIN MUTATED 0 7 2
13Q GAIN WILD-TYPE 60 56 37

Figure S14.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.15

Table S15.  Gene #21: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
13Q GAIN MUTATED 5 1 3
13Q GAIN WILD-TYPE 35 77 41

Figure S15.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00974 (Fisher's exact test), Q value = 0.092

Table S16.  Gene #21: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
13Q GAIN MUTATED 2 0 6 1
13Q GAIN WILD-TYPE 31 64 38 20

Figure S16.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0094 (Fisher's exact test), Q value = 0.091

Table S17.  Gene #21: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
13Q GAIN MUTATED 2 0 6 1
13Q GAIN WILD-TYPE 32 64 37 20

Figure S17.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.16

Table S18.  Gene #21: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
13Q GAIN MUTATED 7 0 2
13Q GAIN WILD-TYPE 58 58 37

Figure S18.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00964 (Fisher's exact test), Q value = 0.092

Table S19.  Gene #21: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
13Q GAIN MUTATED 2 0 0 6 1
13Q GAIN WILD-TYPE 32 58 11 29 22

Figure S19.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.18

Table S20.  Gene #23: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
15Q GAIN MUTATED 3 3 8
15Q GAIN WILD-TYPE 37 75 36

Figure S20.  Get High-res Image Gene #23: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.12

Table S21.  Gene #25: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
16Q GAIN MUTATED 2 0 4
16Q GAIN WILD-TYPE 58 63 35

Figure S21.  Get High-res Image Gene #25: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.21

Table S22.  Gene #28: '18q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
18Q GAIN MUTATED 0 3 2
18Q GAIN WILD-TYPE 31 15 26

Figure S22.  Get High-res Image Gene #28: '18q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.12

Table S23.  Gene #29: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
19P GAIN MUTATED 2 10 8
19P GAIN WILD-TYPE 58 53 31

Figure S23.  Get High-res Image Gene #29: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.0085 (Fisher's exact test), Q value = 0.084

Table S24.  Gene #30: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
19Q GAIN MUTATED 4 2 8
19Q GAIN WILD-TYPE 36 76 36

Figure S24.  Get High-res Image Gene #30: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.18

Table S25.  Gene #32: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
20Q GAIN MUTATED 3 1 6 0
20Q GAIN WILD-TYPE 30 63 38 21

Figure S25.  Get High-res Image Gene #32: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.21

Table S26.  Gene #32: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
20Q GAIN MUTATED 8 1 1
20Q GAIN WILD-TYPE 57 57 38

Figure S26.  Get High-res Image Gene #32: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.21

Table S27.  Gene #32: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
20Q GAIN MUTATED 5 1 0 4 0
20Q GAIN WILD-TYPE 29 57 11 31 23

Figure S27.  Get High-res Image Gene #32: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.13

Table S28.  Gene #35: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
XP GAIN MUTATED 2 0 4
XP GAIN WILD-TYPE 38 78 40

Figure S28.  Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.19

Table S29.  Gene #35: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
XP GAIN MUTATED 3 0 3 0
XP GAIN WILD-TYPE 30 64 41 21

Figure S29.  Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.13

Table S30.  Gene #35: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
XP GAIN MUTATED 4 0 1 1
XP GAIN WILD-TYPE 30 64 42 20

Figure S30.  Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.14

Table S31.  Gene #35: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
XP GAIN MUTATED 4 0 1 1 0
XP GAIN WILD-TYPE 30 58 10 34 23

Figure S31.  Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.22

Table S32.  Gene #36: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
XQ GAIN MUTATED 2 0 3
XQ GAIN WILD-TYPE 38 78 41

Figure S32.  Get High-res Image Gene #36: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.18

Table S33.  Gene #36: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
XQ GAIN MUTATED 4 0 0 1 0
XQ GAIN WILD-TYPE 30 58 11 34 23

Figure S33.  Get High-res Image Gene #36: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S34.  Gene #37: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
1P LOSS MUTATED 51 24 23
1P LOSS WILD-TYPE 9 39 16

Figure S34.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.12

Table S35.  Gene #37: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
1P LOSS MUTATED 19 56 23
1P LOSS WILD-TYPE 21 22 21

Figure S35.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00562 (Fisher's exact test), Q value = 0.064

Table S36.  Gene #37: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
1P LOSS MUTATED 9 6 17 1 7 4
1P LOSS WILD-TYPE 4 3 3 4 10 9

Figure S36.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0046

Table S37.  Gene #37: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
1P LOSS MUTATED 11 17 16
1P LOSS WILD-TYPE 20 1 12

Figure S37.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.037

Table S38.  Gene #37: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
1P LOSS MUTATED 20 49 19 10
1P LOSS WILD-TYPE 13 15 25 11

Figure S38.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.027

Table S39.  Gene #37: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
1P LOSS MUTATED 15 50 23 10
1P LOSS WILD-TYPE 19 14 20 11

Figure S39.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0024

Table S40.  Gene #37: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
1P LOSS MUTATED 29 47 22
1P LOSS WILD-TYPE 36 11 17

Figure S40.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.11

Table S41.  Gene #37: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
1P LOSS MUTATED 31 41 11 15
1P LOSS WILD-TYPE 35 13 7 9

Figure S41.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S42.  Gene #37: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
1P LOSS MUTATED 16 48 6 17 11
1P LOSS WILD-TYPE 18 10 5 18 12

Figure S42.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.18

Table S43.  Gene #38: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
1Q LOSS MUTATED 3 9 0 12 3
1Q LOSS WILD-TYPE 31 49 11 23 20

Figure S43.  Get High-res Image Gene #38: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.00464 (Fisher's exact test), Q value = 0.054

Table S44.  Gene #39: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
2P LOSS MUTATED 0 1 7 2
2P LOSS WILD-TYPE 33 63 37 19

Figure S44.  Get High-res Image Gene #39: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.014

Table S45.  Gene #39: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
2P LOSS MUTATED 3 0 5 2
2P LOSS WILD-TYPE 63 54 13 22

Figure S45.  Get High-res Image Gene #39: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.076

Table S46.  Gene #39: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
2P LOSS MUTATED 3 2 5 0
2P LOSS WILD-TYPE 68 51 13 19

Figure S46.  Get High-res Image Gene #39: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.012

Table S47.  Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
3P LOSS MUTATED 17 20 25
3P LOSS WILD-TYPE 43 43 14

Figure S47.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0034 (Fisher's exact test), Q value = 0.042

Table S48.  Gene #41: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
3P LOSS MUTATED 1 2 9 4 4 9
3P LOSS WILD-TYPE 12 7 11 1 13 4

Figure S48.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0084

Table S49.  Gene #41: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
3P LOSS MUTATED 16 19 25 2
3P LOSS WILD-TYPE 17 45 19 19

Figure S49.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S50.  Gene #41: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
3P LOSS MUTATED 9 21 30 2
3P LOSS WILD-TYPE 25 43 13 19

Figure S50.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.016

Table S51.  Gene #41: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
3P LOSS MUTATED 35 20 7
3P LOSS WILD-TYPE 30 38 32

Figure S51.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.02

Table S52.  Gene #41: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
3P LOSS MUTATED 36 17 6 3
3P LOSS WILD-TYPE 30 37 12 21

Figure S52.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0075

Table S53.  Gene #41: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
3P LOSS MUTATED 13 16 2 25 6
3P LOSS WILD-TYPE 21 42 9 10 17

Figure S53.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0065

Table S54.  Gene #41: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
3P LOSS MUTATED 20 33 6 3
3P LOSS WILD-TYPE 51 20 12 16

Figure S54.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0024

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
3Q LOSS MUTATED 36 22 30
3Q LOSS WILD-TYPE 24 41 9

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

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.16

Table S56.  Gene #42: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
3Q LOSS MUTATED 11 13 17
3Q LOSS WILD-TYPE 20 5 11

Figure S56.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.22

Table S57.  Gene #42: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
3Q LOSS MUTATED 20 40 22 6
3Q LOSS WILD-TYPE 13 24 22 15

Figure S57.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S58.  Gene #42: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
3Q LOSS MUTATED 6 42 33 7
3Q LOSS WILD-TYPE 28 22 10 14

Figure S58.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00354 (Fisher's exact test), Q value = 0.043

Table S59.  Gene #42: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
3Q LOSS MUTATED 39 37 12
3Q LOSS WILD-TYPE 26 21 27

Figure S59.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.18

Table S60.  Gene #42: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
3Q LOSS MUTATED 39 34 5 10
3Q LOSS WILD-TYPE 27 20 13 14

Figure S60.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.11

Table S61.  Gene #42: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
3Q LOSS MUTATED 11 38 4 23 12
3Q LOSS WILD-TYPE 23 20 7 12 11

Figure S61.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.13

Table S62.  Gene #42: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
3Q LOSS MUTATED 39 36 5 8
3Q LOSS WILD-TYPE 32 17 13 11

Figure S62.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.042

Table S63.  Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
4P LOSS MUTATED 0 5 6
4P LOSS WILD-TYPE 60 58 33

Figure S63.  Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0068 (Fisher's exact test), Q value = 0.073

Table S64.  Gene #43: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
4P LOSS MUTATED 0 3 8 0
4P LOSS WILD-TYPE 33 61 36 21

Figure S64.  Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.13

Table S65.  Gene #44: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
4Q LOSS MUTATED 0 3 7 0
4Q LOSS WILD-TYPE 33 61 37 21

Figure S65.  Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.2

Table S66.  Gene #45: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
5P LOSS MUTATED 1 0 4 0
5P LOSS WILD-TYPE 32 64 40 21

Figure S66.  Get High-res Image Gene #45: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.2

Table S67.  Gene #45: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
5P LOSS MUTATED 1 0 4 0
5P LOSS WILD-TYPE 33 64 39 21

Figure S67.  Get High-res Image Gene #45: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.017

Table S68.  Gene #47: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
6Q LOSS MUTATED 13 1 5
6Q LOSS WILD-TYPE 47 62 34

Figure S68.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.012

Table S69.  Gene #47: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
6Q LOSS MUTATED 1 17 1
6Q LOSS WILD-TYPE 39 61 43

Figure S69.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.14

Table S70.  Gene #47: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
6Q LOSS MUTATED 2 1 8 0 0 1
6Q LOSS WILD-TYPE 11 8 12 5 17 12

Figure S70.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.012

Table S71.  Gene #47: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
6Q LOSS MUTATED 1 16 1 1
6Q LOSS WILD-TYPE 32 48 43 20

Figure S71.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0024

Table S72.  Gene #47: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
6Q LOSS MUTATED 0 17 1 1
6Q LOSS WILD-TYPE 34 47 42 20

Figure S72.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0084

Table S73.  Gene #47: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
6Q LOSS MUTATED 1 14 4
6Q LOSS WILD-TYPE 64 44 35

Figure S73.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S74.  Gene #47: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
6Q LOSS MUTATED 1 16 1 1
6Q LOSS WILD-TYPE 65 38 17 23

Figure S74.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.11

Table S75.  Gene #47: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
6Q LOSS MUTATED 2 14 1 1 1
6Q LOSS WILD-TYPE 32 44 10 34 22

Figure S75.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.032

Table S76.  Gene #47: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
6Q LOSS MUTATED 16 1 1 1
6Q LOSS WILD-TYPE 55 52 17 18

Figure S76.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.18

Table S77.  Gene #48: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
7Q LOSS MUTATED 5 0 1
7Q LOSS WILD-TYPE 55 63 38

Figure S77.  Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.21

Table S78.  Gene #48: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
7Q LOSS MUTATED 0 6 0 0
7Q LOSS WILD-TYPE 33 58 44 21

Figure S78.  Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.18

Table S79.  Gene #48: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
7Q LOSS MUTATED 0 5 1
7Q LOSS WILD-TYPE 65 53 38

Figure S79.  Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.16

Table S80.  Gene #48: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
7Q LOSS MUTATED 0 5 1 0
7Q LOSS WILD-TYPE 66 49 17 24

Figure S80.  Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.15

Table S81.  Gene #49: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
8P LOSS MUTATED 8 3 9
8P LOSS WILD-TYPE 52 60 30

Figure S81.  Get High-res Image Gene #49: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.22

Table S82.  Gene #50: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
8Q LOSS MUTATED 6 1 5
8Q LOSS WILD-TYPE 54 62 34

Figure S82.  Get High-res Image Gene #50: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.24

Table S83.  Gene #51: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
9P LOSS MUTATED 5 1 5
9P LOSS WILD-TYPE 55 62 34

Figure S83.  Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.13

Table S84.  Gene #51: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
9P LOSS MUTATED 0 0 4
9P LOSS WILD-TYPE 31 18 24

Figure S84.  Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00786 (Fisher's exact test), Q value = 0.079

Table S85.  Gene #52: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
9Q LOSS MUTATED 3 1 7
9Q LOSS WILD-TYPE 57 62 32

Figure S85.  Get High-res Image Gene #52: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S86.  Gene #53: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
11P LOSS MUTATED 1 36 17
11P LOSS WILD-TYPE 59 27 22

Figure S86.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.012

Table S87.  Gene #53: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
11P LOSS MUTATED 21 15 18
11P LOSS WILD-TYPE 19 63 26

Figure S87.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.019

Table S88.  Gene #53: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
11P LOSS MUTATED 3 1 2 3 9 9
11P LOSS WILD-TYPE 10 8 18 2 8 4

Figure S88.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0075

Table S89.  Gene #53: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
11P LOSS MUTATED 12 11 25 6
11P LOSS WILD-TYPE 21 53 19 15

Figure S89.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S90.  Gene #53: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
11P LOSS MUTATED 11 9 28 6
11P LOSS WILD-TYPE 23 55 15 15

Figure S90.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0017

Table S91.  Gene #53: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
11P LOSS MUTATED 34 9 11
11P LOSS WILD-TYPE 31 49 28

Figure S91.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S92.  Gene #53: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
11P LOSS MUTATED 37 6 5 6
11P LOSS WILD-TYPE 29 48 13 18

Figure S92.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0024

Table S93.  Gene #53: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
11P LOSS MUTATED 12 7 3 20 11
11P LOSS WILD-TYPE 22 51 8 15 12

Figure S93.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.033

Table S94.  Gene #53: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
11P LOSS MUTATED 15 28 5 5
11P LOSS WILD-TYPE 56 25 13 14

Figure S94.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S95.  Gene #54: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
11Q LOSS MUTATED 3 24 13
11Q LOSS WILD-TYPE 57 39 26

Figure S95.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'RPPA_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.15

Table S96.  Gene #54: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
11Q LOSS MUTATED 4 1 4 2 9 9
11Q LOSS WILD-TYPE 9 8 16 3 8 4

Figure S96.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0075

Table S97.  Gene #54: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
11Q LOSS MUTATED 8 7 21 4
11Q LOSS WILD-TYPE 25 57 23 17

Figure S97.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.014

Table S98.  Gene #54: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
11Q LOSS MUTATED 9 8 20 3
11Q LOSS WILD-TYPE 25 56 23 18

Figure S98.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0066

Table S99.  Gene #54: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
11Q LOSS MUTATED 26 5 9
11Q LOSS WILD-TYPE 39 53 30

Figure S99.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0084

Table S100.  Gene #54: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
11Q LOSS MUTATED 27 5 2 6
11Q LOSS WILD-TYPE 39 49 16 18

Figure S100.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0066

Table S101.  Gene #54: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
11Q LOSS MUTATED 9 5 2 18 6
11Q LOSS WILD-TYPE 25 53 9 17 17

Figure S101.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.16

Table S102.  Gene #54: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
11Q LOSS MUTATED 13 21 2 4
11Q LOSS WILD-TYPE 58 32 16 15

Figure S102.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.2

Table S103.  Gene #55: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
13Q LOSS MUTATED 5 0 3
13Q LOSS WILD-TYPE 55 63 36

Figure S103.  Get High-res Image Gene #55: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.11

Table S104.  Gene #55: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
13Q LOSS MUTATED 0 1 0 2 1 0
13Q LOSS WILD-TYPE 13 8 20 3 16 13

Figure S104.  Get High-res Image Gene #55: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00198 (Fisher's exact test), Q value = 0.028

Table S105.  Gene #56: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
14Q LOSS MUTATED 5 5 8 2
14Q LOSS WILD-TYPE 61 49 10 22

Figure S105.  Get High-res Image Gene #56: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.18

Table S106.  Gene #56: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
14Q LOSS MUTATED 10 4 0 4 2
14Q LOSS WILD-TYPE 24 54 11 31 21

Figure S106.  Get High-res Image Gene #56: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.025

Table S107.  Gene #56: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
14Q LOSS MUTATED 5 5 8 2
14Q LOSS WILD-TYPE 66 48 10 17

Figure S107.  Get High-res Image Gene #56: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.22

Table S108.  Gene #58: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
16P LOSS MUTATED 5 4 0
16P LOSS WILD-TYPE 35 74 44

Figure S108.  Get High-res Image Gene #58: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.17

Table S109.  Gene #59: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
16Q LOSS MUTATED 4 1 0 0
16Q LOSS WILD-TYPE 30 63 43 21

Figure S109.  Get High-res Image Gene #59: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.012

Table S110.  Gene #60: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
17P LOSS MUTATED 20 16 25
17P LOSS WILD-TYPE 40 47 14

Figure S110.  Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.032

Table S111.  Gene #60: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
17P LOSS MUTATED 9 40 12
17P LOSS WILD-TYPE 31 38 32

Figure S111.  Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.19

Table S112.  Gene #60: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
17P LOSS MUTATED 10 33 13 5
17P LOSS WILD-TYPE 24 31 30 16

Figure S112.  Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.15

Table S113.  Gene #60: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
17P LOSS MUTATED 20 30 11
17P LOSS WILD-TYPE 45 28 28

Figure S113.  Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.15

Table S114.  Gene #60: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
17P LOSS MUTATED 18 29 7 7
17P LOSS WILD-TYPE 48 25 11 17

Figure S114.  Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.12

Table S115.  Gene #60: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
17P LOSS MUTATED 36 12 7 6
17P LOSS WILD-TYPE 35 41 11 13

Figure S115.  Get High-res Image Gene #60: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0024

Table S116.  Gene #61: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
17Q LOSS MUTATED 4 2 13
17Q LOSS WILD-TYPE 56 61 26

Figure S116.  Get High-res Image Gene #61: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.18

Table S117.  Gene #61: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
17Q LOSS MUTATED 1 1 7
17Q LOSS WILD-TYPE 30 17 21

Figure S117.  Get High-res Image Gene #61: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.21

Table S118.  Gene #66: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
21Q LOSS MUTATED 2 15 14 5
21Q LOSS WILD-TYPE 31 49 30 16

Figure S118.  Get High-res Image Gene #66: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S119.  Gene #67: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
22Q LOSS MUTATED 35 8 15
22Q LOSS WILD-TYPE 25 55 24

Figure S119.  Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.11

Table S120.  Gene #67: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
22Q LOSS MUTATED 10 37 11
22Q LOSS WILD-TYPE 30 41 33

Figure S120.  Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.18

Table S121.  Gene #67: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
22Q LOSS MUTATED 9 31 10 8
22Q LOSS WILD-TYPE 24 33 34 13

Figure S121.  Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.029

Table S122.  Gene #67: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
22Q LOSS MUTATED 11 33 7 7
22Q LOSS WILD-TYPE 23 31 36 14

Figure S122.  Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.24

Table S123.  Gene #67: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
22Q LOSS MUTATED 16 25 17
22Q LOSS WILD-TYPE 49 33 22

Figure S123.  Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.17

Table S124.  Gene #67: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
22Q LOSS MUTATED 12 29 4 6 7
22Q LOSS WILD-TYPE 22 29 7 29 16

Figure S124.  Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.16

Table S125.  Gene #67: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
22Q LOSS MUTATED 33 11 6 8
22Q LOSS WILD-TYPE 38 42 12 11

Figure S125.  Get High-res Image Gene #67: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S126.  Gene #68: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
XP LOSS MUTATED 22 7 19
XP LOSS WILD-TYPE 38 56 20

Figure S126.  Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.027

Table S127.  Gene #68: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
XP LOSS MUTATED 9 33 6
XP LOSS WILD-TYPE 31 45 38

Figure S127.  Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.11

Table S128.  Gene #68: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
XP LOSS MUTATED 10 27 9 2
XP LOSS WILD-TYPE 23 37 35 19

Figure S128.  Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.017

Table S129.  Gene #68: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
XP LOSS MUTATED 7 29 11 1
XP LOSS WILD-TYPE 27 35 32 20

Figure S129.  Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.033

Table S130.  Gene #68: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
XP LOSS MUTATED 13 27 8
XP LOSS WILD-TYPE 52 31 31

Figure S130.  Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.13

Table S131.  Gene #68: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
XP LOSS MUTATED 15 23 7 3
XP LOSS WILD-TYPE 51 31 11 21

Figure S131.  Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.13

Table S132.  Gene #68: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
XP LOSS MUTATED 27 13 7 1
XP LOSS WILD-TYPE 44 40 11 18

Figure S132.  Get High-res Image Gene #68: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0017

Table S133.  Gene #69: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
XQ LOSS MUTATED 22 7 20
XQ LOSS WILD-TYPE 38 56 19

Figure S133.  Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.022

Table S134.  Gene #69: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
XQ LOSS MUTATED 9 34 6
XQ LOSS WILD-TYPE 31 44 38

Figure S134.  Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00735 (Fisher's exact test), Q value = 0.076

Table S135.  Gene #69: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
XQ LOSS MUTATED 10 28 9 2
XQ LOSS WILD-TYPE 23 36 35 19

Figure S135.  Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.012

Table S136.  Gene #69: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
XQ LOSS MUTATED 7 30 11 1
XQ LOSS WILD-TYPE 27 34 32 20

Figure S136.  Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.045

Table S137.  Gene #69: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
XQ LOSS MUTATED 13 27 9
XQ LOSS WILD-TYPE 52 31 30

Figure S137.  Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.097

Table S138.  Gene #69: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
XQ LOSS MUTATED 15 24 7 3
XQ LOSS WILD-TYPE 51 30 11 21

Figure S138.  Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.11

Table S139.  Gene #69: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
XQ LOSS MUTATED 28 13 7 1
XQ LOSS WILD-TYPE 43 40 11 18

Figure S139.  Get High-res Image Gene #69: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/PCPG-TP/15096455/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/15107813/PCPG-TP.transferedmergedcluster.txt

  • Number of patients = 162

  • Number of significantly arm-level cnvs = 69

  • 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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