Correlation between copy number variations of arm-level result and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1RN379H
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1RN379H
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 70 arm-level events and 10 molecular subtypes across 162 patients, 128 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 2p gain cnv correlated to 'METHLYATION_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'METHLYATION_CNMF'.

  • 7q gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'CN_CNMF'.

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

  • 12q gain cnv correlated to 'MIRSEQ_CNMF'.

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

  • 18q gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'METHLYATION_CNMF'.

  • 20q gain cnv correlated to 'MIRSEQ_CNMF'.

  • 22q gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • 1q loss cnv correlated to 'RPPA_CHIERARCHICAL'.

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

  • 3p loss cnv correlated to 'CN_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_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 12p loss cnv correlated to 'CN_CNMF'.

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

  • 16q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 21q loss cnv correlated to 'METHLYATION_CNMF'.

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

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

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_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 70 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, 128 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 97 (60%) 65 2e-05
(0.0014) 		0.00372
(0.0476) 		0.122
(0.424) 		5e-05
(0.00219) 		0.00717
(0.0797) 		0.00378
(0.0476) 		0.00028
(0.00891) 		0.0255
(0.184) 		0.00064
(0.0125) 		0.00282
(0.038)
6q loss 18 (11%) 144 0.00041
(0.0106) 		0.00043
(0.0107) 		0.0398
(0.223) 		0.216
(0.555) 		0.00154
(0.0234) 		7e-05
(0.00258) 		0.00049
(0.0114) 		4e-05
(0.00219) 		0.062
(0.303) 		0.00121
(0.0192)
11p loss 54 (33%) 108 0.0217
(0.164) 		0.00033
(0.00962) 		0.0538
(0.283) 		0.141
(0.455) 		0.00065
(0.0125) 		1e-05
(0.001) 		5e-05
(0.00219) 		1e-05
(0.001) 		0.00022
(0.00733) 		1e-05
(0.001)
11q loss 40 (25%) 122 2e-05
(0.0014) 		0.0297
(0.192) 		0.155
(0.467) 		0.115
(0.417) 		0.00064
(0.0125) 		0.00082
(0.014) 		5e-05
(0.00219) 		0.00036
(0.00996) 		0.00037
(0.00996) 		3e-05
(0.00191)
xp loss 48 (30%) 114 0.00017
(0.00595) 		6e-05
(0.00233) 		0.0363
(0.217) 		0.441
(0.756) 		0.0148
(0.13) 		0.00108
(0.0176) 		0.0007
(0.0129) 		0.0177
(0.147) 		0.276
(0.629) 		0.00839
(0.089)
xq loss 49 (30%) 113 6e-05
(0.00233) 		5e-05
(0.00219) 		0.0239
(0.176) 		0.611
(0.855) 		0.00932
(0.0945) 		0.00058
(0.0125) 		0.00125
(0.0194) 		0.0103
(0.103) 		0.36
(0.69) 		0.00415
(0.051)
3p loss 60 (37%) 102 0.0137
(0.128) 		0.156
(0.467) 		0.224
(0.567) 		0.547
(0.822) 		0.0003
(0.00913) 		1e-05
(0.001) 		0.00055
(0.0124) 		0.00381
(0.0476) 		0.00079
(0.0138) 		2e-05
(0.0014)
3q loss 87 (54%) 75 1e-05
(0.001) 		0.979
(1.00) 		0.0677
(0.312) 		0.0257
(0.184) 		0.055
(0.283) 		1e-05
(0.001) 		0.00077
(0.0138) 		0.043
(0.237) 		0.0038
(0.0476) 		0.00049
(0.0114)
17p loss 62 (38%) 100 0.00091
(0.0152) 		0.00226
(0.0316) 		0.36
(0.69) 		0.146
(0.458) 		0.0268
(0.187) 		0.0199
(0.157) 		0.0255
(0.184) 		0.0184
(0.148) 		0.124
(0.428) 		0.0351
(0.216)
13q gain 9 (6%) 153 0.038
(0.22) 		0.0563
(0.283) 		0.305
(0.653) 		0.623
(0.864) 		0.00885
(0.0925) 		0.00911
(0.0938) 		0.0212
(0.163) 		0.0545
(0.283) 		0.0077
(0.0841) 		0.00474
(0.0562)
22q loss 58 (36%) 104 1e-05
(0.001) 		0.0207
(0.161) 		0.554
(0.822) 		0.0846
(0.355) 		0.0179
(0.147) 		0.0022
(0.0314) 		0.0319
(0.205) 		0.052
(0.278) 		0.0342
(0.213) 		0.101
(0.393)
12p gain 11 (7%) 151 0.236
(0.579) 		0.00513
(0.0589) 		0.476
(0.778) 		0.118
(0.417) 		0.61
(0.855) 		0.322
(0.665) 		0.014
(0.128) 		0.212
(0.546) 		0.0118
(0.113) 		0.0278
(0.191)
8p gain 9 (6%) 153 0.155
(0.467) 		0.238
(0.581) 		0.4
(0.722) 		1
(1.00) 		0.0635
(0.305) 		0.0132
(0.125) 		0.0292
(0.192) 		0.0385
(0.22) 		0.417
(0.733) 		0.0925
(0.376)
xp gain 6 (4%) 156 0.163
(0.473) 		0.101
(0.393) 		0.337
(0.673) 		0.0155
(0.133) 		0.175
(0.497) 		0.07
(0.316) 		0.0289
(0.192) 		0.0145
(0.128)
2p loss 10 (6%) 152 0.15
(0.463) 		0.067
(0.312) 		0.755
(0.937) 		0.428
(0.743) 		0.00489
(0.057) 		0.181
(0.504) 		0.291
(0.64) 		0.00065
(0.0125) 		0.293
(0.64) 		0.0115
(0.112)
4p loss 11 (7%) 151 0.00462
(0.0558) 		0.146
(0.458) 		0.609
(0.855) 		0.35
(0.683) 		0.00781
(0.0841) 		0.182
(0.504) 		0.277
(0.629) 		0.393
(0.718) 		0.071
(0.316) 		0.0294
(0.192)
7q loss 7 (4%) 155 0.405
(0.725) 		0.318
(0.664) 		0.192
(0.518) 		0.113
(0.417) 		0.0223
(0.166) 		0.101
(0.393) 		0.0284
(0.192) 		0.0115
(0.112) 		0.243
(0.584) 		0.159
(0.468)
1q gain 19 (12%) 143 0.0153
(0.132) 		0.038
(0.22) 		0.766
(0.937) 		1
(1.00) 		0.477
(0.778) 		0.422
(0.738) 		0.644
(0.872) 		0.682
(0.897) 		0.504
(0.797) 		0.578
(0.842)
xq gain 5 (3%) 157 0.292
(0.64) 		0.253
(0.596) 		0.545
(0.822) 		0.0554
(0.283) 		0.186
(0.511) 		0.0681
(0.312) 		0.0215
(0.163) 		0.00249
(0.0342)
5p loss 5 (3%) 157 0.728
(0.927) 		0.446
(0.759) 		0.036
(0.217) 		0.0361
(0.217) 		0.184
(0.508) 		0.166
(0.479) 		0.245
(0.585) 		0.0914
(0.374)
9p loss 11 (7%) 151 0.177
(0.503) 		0.4
(0.722) 		0.0143
(0.128) 		0.0181
(0.147) 		0.193
(0.519) 		0.179
(0.503) 		0.627
(0.864) 		0.0678
(0.312) 		0.263
(0.611) 		0.0744
(0.324)
14q loss 20 (12%) 142 0.727
(0.927) 		0.248
(0.586) 		0.241
(0.582) 		0.203
(0.537) 		0.32
(0.665) 		0.793
(0.938) 		0.28
(0.635) 		0.00162
(0.0241) 		0.0626
(0.303) 		0.00066
(0.0125)
2p gain 6 (4%) 156 0.309
(0.657) 		0.00604
(0.0682) 		0.0885
(0.366) 		1
(1.00) 		0.237
(0.579) 		0.345
(0.68) 		0.106
(0.405) 		0.337
(0.673) 		0.108
(0.411) 		0.195
(0.522)
4q gain 3 (2%) 159 0.014
(0.128) 		0.801
(0.94) 		0.467
(0.778) 		0.742
(0.937) 		0.628
(0.864) 		0.837
(0.962) 		0.78
(0.937) 		0.899
(1.00)
5q gain 7 (4%) 155 0.969
(1.00) 		0.002
(0.0292) 		0.0713
(0.316) 		0.297
(0.645) 		0.555
(0.822) 		0.382
(0.707) 		1
(1.00) 		0.476
(0.778)
7q gain 21 (13%) 141 0.265
(0.611) 		0.0555
(0.283) 		0.909
(1.00) 		0.0442
(0.242) 		0.135
(0.446) 		0.158
(0.468) 		0.0795
(0.337) 		0.179
(0.503) 		0.502
(0.796) 		0.385
(0.711)
11p gain 5 (3%) 157 0.0384
(0.22) 		0.516
(0.803) 		0.548
(0.822) 		1
(1.00) 		0.509
(0.797) 		0.302
(0.648) 		0.527
(0.807) 		0.495
(0.788) 		0.0594
(0.293) 		0.335
(0.673)
12q gain 14 (9%) 148 0.153
(0.467) 		0.135
(0.446) 		0.841
(0.964) 		0.494
(0.788) 		0.667
(0.884) 		0.656
(0.88) 		0.0338
(0.213) 		0.292
(0.64) 		0.0549
(0.283) 		0.163
(0.473)
18q gain 10 (6%) 152 0.366
(0.692) 		0.915
(1.00) 		0.476
(0.778) 		0.0386
(0.22) 		0.374
(0.698) 		0.536
(0.817) 		0.779
(0.937) 		0.435
(0.751) 		0.126
(0.431) 		0.719
(0.924)
19q gain 14 (9%) 148 0.0667
(0.312) 		0.0338
(0.213) 		0.0877
(0.365) 		0.541
(0.822) 		0.547
(0.822) 		0.226
(0.567) 		0.599
(0.848) 		0.664
(0.883) 		0.583
(0.844) 		0.189
(0.514)
20q gain 10 (6%) 152 0.712
(0.918) 		0.492
(0.788) 		0.155
(0.467) 		1
(1.00) 		0.109
(0.414) 		0.0627
(0.303) 		0.0344
(0.213) 		0.0768
(0.33) 		0.0784
(0.335) 		0.228
(0.567)
22q gain 3 (2%) 159 0.62
(0.863) 		0.144
(0.455) 		0.231
(0.571) 		0.148
(0.462) 		0.114
(0.417) 		0.409
(0.726) 		0.0392
(0.221) 		0.494
(0.788)
1q loss 25 (15%) 137 0.393
(0.718) 		0.591
(0.845) 		1
(1.00) 		0.043
(0.237) 		0.128
(0.437) 		0.578
(0.842) 		0.476
(0.778) 		0.195
(0.522) 		0.159
(0.468) 		0.523
(0.805)
4q loss 10 (6%) 152 0.0968
(0.388) 		0.246
(0.585) 		0.612
(0.856) 		0.35
(0.683) 		0.0195
(0.155) 		0.339
(0.673) 		0.321
(0.665) 		0.525
(0.806) 		0.288
(0.64) 		0.0896
(0.369)
12p loss 3 (2%) 159 0.0278
(0.191) 		0.335
(0.673) 		0.368
(0.692) 		0.787
(0.937) 		0.642
(0.872) 		0.291
(0.64) 		0.784
(0.937) 		1
(1.00) 		0.047
(0.255) 		0.651
(0.876)
16q loss 5 (3%) 157 0.907
(1.00) 		1
(1.00) 		0.697
(0.904) 		0.786
(0.937) 		0.41
(0.727) 		0.0268
(0.187) 		0.264
(0.611) 		0.591
(0.845) 		0.329
(0.671) 		0.647
(0.872)
18p loss 16 (10%) 146 0.0296
(0.192) 		0.742
(0.937) 		0.725
(0.927) 		0.209
(0.546) 		0.829
(0.958) 		0.754
(0.937) 		0.799
(0.94) 		0.314
(0.661) 		0.483
(0.785) 		0.552
(0.822)
19q loss 5 (3%) 157 0.791
(0.938) 		0.847
(0.969) 		1
(1.00) 		1
(1.00) 		0.313
(0.661) 		0.772
(0.937) 		0.0381
(0.22) 		0.893
(1.00)
21q loss 36 (22%) 126 0.17
(0.487) 		0.0178
(0.147) 		0.945
(1.00) 		0.455
(0.766) 		0.0488
(0.263) 		0.938
(1.00) 		0.838
(0.962) 		0.603
(0.852) 		0.918
(1.00) 		0.299
(0.646)
1p gain 6 (4%) 156 0.64
(0.872) 		0.131
(0.445) 		0.785
(0.937) 		0.943
(1.00) 		0.332
(0.673) 		0.764
(0.937) 		0.76
(0.937) 		0.963
(1.00)
4p gain 4 (2%) 158 0.255
(0.597) 		0.368
(0.692) 		0.751
(0.937) 		0.555
(0.822) 		0.458
(0.769) 		0.787
(0.937) 		0.805
(0.94) 		0.963
(1.00)
5p gain 11 (7%) 151 0.869
(0.985) 		0.143
(0.455) 		0.487
(0.787) 		1
(1.00) 		0.942
(1.00) 		0.66
(0.882) 		0.924
(1.00) 		0.614
(0.856) 		0.634
(0.87) 		0.851
(0.97)
6p gain 14 (9%) 148 0.566
(0.828) 		0.359
(0.69) 		0.156
(0.467) 		0.2
(0.532) 		0.425
(0.742) 		0.105
(0.404) 		0.172
(0.492) 		0.302
(0.648) 		0.692
(0.901) 		0.272
(0.622)
6q gain 8 (5%) 154 0.184
(0.508) 		0.12
(0.419) 		0.887
(1.00) 		0.115
(0.417) 		0.211
(0.546) 		0.0992
(0.392) 		0.475
(0.778) 		0.562
(0.826) 		0.246
(0.585) 		0.0957
(0.387)
7p gain 27 (17%) 135 0.413
(0.728) 		0.18
(0.504) 		0.849
(0.97) 		0.149
(0.463) 		0.141
(0.455) 		0.378
(0.703) 		0.369
(0.692) 		0.0713
(0.316) 		0.228
(0.567) 		0.0558
(0.283)
8q gain 13 (8%) 149 0.227
(0.567) 		0.753
(0.937) 		0.593
(0.845) 		1
(1.00) 		0.104
(0.402) 		0.0758
(0.328) 		0.189
(0.514) 		0.201
(0.532) 		0.804
(0.94) 		0.428
(0.743)
9p gain 4 (2%) 158 0.766
(0.937) 		0.69
(0.901) 		0.15
(0.463) 		0.224
(0.567) 		0.308
(0.657) 		0.255
(0.597) 		0.358
(0.69) 		0.468
(0.778)
9q gain 3 (2%) 159 0.821
(0.951) 		0.444
(0.759) 		0.229
(0.568) 		0.239
(0.581) 		0.491
(0.788) 		0.343
(0.679) 		0.286
(0.64) 		0.297
(0.645)
10p gain 12 (7%) 150 0.717
(0.923) 		0.0725
(0.319) 		1
(1.00) 		0.119
(0.417) 		0.854
(0.972) 		0.516
(0.803) 		1
(1.00) 		0.838
(0.962) 		0.824
(0.953) 		0.133
(0.446)
10q gain 10 (6%) 152 0.544
(0.822) 		0.244
(0.584) 		1
(1.00) 		0.12
(0.419) 		0.578
(0.842) 		0.594
(0.845) 		0.604
(0.852) 		0.51
(0.797) 		0.789
(0.938) 		0.143
(0.455)
14q gain 4 (2%) 158 0.553
(0.822) 		0.688
(0.901) 		1
(1.00) 		0.553
(0.822) 		0.313
(0.661) 		0.787
(0.937) 		0.806
(0.94) 		0.338
(0.673)
15q gain 14 (9%) 148 0.066
(0.312) 		0.133
(0.446) 		0.663
(0.883) 		0.35
(0.683) 		0.27
(0.62) 		0.768
(0.937) 		0.314
(0.661) 		0.792
(0.938) 		0.362
(0.69) 		0.593
(0.845)
16p gain 6 (4%) 156 0.586
(0.845) 		0.555
(0.822) 		0.785
(0.937) 		0.742
(0.937) 		0.51
(0.797) 		0.819
(0.951) 		0.468
(0.778) 		0.523
(0.805)
16q gain 6 (4%) 156 0.118
(0.417) 		1
(1.00) 		0.159
(0.468) 		0.698
(0.904) 		0.669
(0.885) 		0.765
(0.937) 		0.759
(0.937) 		0.361
(0.69)
17q gain 6 (4%) 156 0.635
(0.87) 		0.134
(0.446) 		0.16
(0.468) 		0.698
(0.904) 		0.33
(0.672) 		0.768
(0.937) 		0.448
(0.761) 		0.71
(0.917)
18p gain 8 (5%) 154 0.136
(0.446) 		0.657
(0.88) 		0.435
(0.751) 		0.118
(0.417) 		0.519
(0.805) 		0.647
(0.872) 		0.474
(0.778) 		0.562
(0.826) 		0.0985
(0.392) 		0.751
(0.937)
19p gain 20 (12%) 142 0.21
(0.546) 		0.14
(0.455) 		0.865
(0.981) 		0.781
(0.937) 		0.802
(0.94) 		0.645
(0.872) 		0.324
(0.667) 		0.924
(1.00) 		0.264
(0.611) 		0.411
(0.727)
20p gain 12 (7%) 150 0.453
(0.764) 		0.742
(0.937) 		0.265
(0.611) 		0.726
(0.927) 		0.293
(0.64) 		0.341
(0.677) 		0.117
(0.417) 		0.382
(0.707) 		0.76
(0.937) 		0.692
(0.901)
21q gain 3 (2%) 159 0.82
(0.951) 		0.143
(0.455) 		0.232
(0.572) 		0.0683
(0.312) 		0.113
(0.417) 		0.406
(0.725) 		0.287
(0.64) 		0.116
(0.417)
2q loss 13 (8%) 149 0.914
(1.00) 		0.452
(0.764) 		0.682
(0.897) 		0.429
(0.744) 		0.406
(0.725) 		0.142
(0.455) 		0.761
(0.937) 		0.0971
(0.388) 		0.282
(0.636) 		0.508
(0.797)
5q loss 7 (4%) 155 0.503
(0.796) 		0.781
(0.937) 		0.326
(0.667) 		1
(1.00) 		0.645
(0.872) 		0.524
(0.805) 		0.795
(0.939) 		0.358
(0.69) 		0.582
(0.844) 		0.59
(0.845)
8p loss 21 (13%) 141 0.114
(0.417) 		0.597
(0.848) 		0.727
(0.927) 		0.756
(0.937) 		0.0832
(0.351) 		0.0732
(0.32) 		0.387
(0.711) 		0.814
(0.949) 		0.449
(0.761) 		0.286
(0.64)
8q loss 12 (7%) 150 0.151
(0.465) 		0.926
(1.00) 		0.483
(0.785) 		1
(1.00) 		0.325
(0.667) 		0.622
(0.864) 		0.0569
(0.283) 		0.439
(0.756) 		0.876
(0.989) 		0.374
(0.698)
9q loss 12 (7%) 150 0.558
(0.824) 		0.191
(0.518) 		0.241
(0.582) 		0.349
(0.683) 		0.387
(0.711) 		0.486
(0.787) 		0.751
(0.937) 		0.295
(0.642) 		0.61
(0.855) 		0.689
(0.901)
13q loss 8 (5%) 154 0.771
(0.937) 		0.407
(0.725) 		0.774
(0.937) 		0.671
(0.887) 		0.317
(0.663) 		0.116
(0.417) 		0.666
(0.884) 		0.226
(0.567) 		0.397
(0.721) 		0.489
(0.788)
15q loss 3 (2%) 159 0.75
(0.937) 		1
(1.00) 		1
(1.00) 		0.864
(0.981) 		0.627
(0.864) 		0.832
(0.959) 		0.563
(0.826) 		0.625
(0.864)
16p loss 9 (6%) 153 0.523
(0.805) 		0.322
(0.665) 		0.477
(0.778) 		0.445
(0.759) 		0.534
(0.816) 		0.363
(0.69) 		0.226
(0.567) 		0.405
(0.725) 		0.803
(0.94) 		0.354
(0.688)
17q loss 15 (9%) 147 0.132
(0.445) 		0.11
(0.415) 		0.205
(0.54) 		0.0687
(0.312) 		0.215
(0.553) 		0.495
(0.788) 		0.748
(0.937) 		0.365
(0.692) 		0.399
(0.722) 		0.17
(0.487)
18q loss 6 (4%) 156 0.474
(0.778) 		0.873
(0.988) 		0.549
(0.822) 		0.057
(0.283) 		0.587
(0.845) 		0.66
(0.882) 		0.506
(0.797) 		0.584
(0.844) 		0.42
(0.737) 		0.685
(0.9)
20q loss 3 (2%) 159 0.337
(0.673) 		1
(1.00) 		1
(1.00) 		0.641
(0.872) 		0.782
(0.937) 		1
(1.00) 		0.211
(0.546) 		0.396
(0.721)
'1q gain' versus 'CN_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
1Q GAIN MUTATED 10 1 0 6 2
1Q GAIN WILD-TYPE 27 39 10 44 23

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
1Q GAIN MUTATED 9 8 2
1Q GAIN WILD-TYPE 31 69 43

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00604 (Fisher's exact test), Q value = 0.068

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
2P GAIN MUTATED 5 1 0
2P GAIN WILD-TYPE 35 76 45

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
4Q GAIN MUTATED 0 0 0 0 3
4Q GAIN WILD-TYPE 37 40 10 50 22

Figure S4.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.029

Table S5.  Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
5Q GAIN MUTATED 1 0 6
5Q GAIN WILD-TYPE 39 77 39

Figure S5.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 0.24

Table S6.  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 7
7Q GAIN WILD-TYPE 30 16 21

Figure S6.  Get High-res Image Gene #11: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.13

Table S7.  Gene #12: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
8P GAIN MUTATED 3 0 3 3
8P GAIN WILD-TYPE 31 64 40 18

Figure S7.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.19

Table S8.  Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
8P GAIN MUTATED 4 5 0
8P GAIN WILD-TYPE 59 39 55

Figure S8.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.22

Table S9.  Gene #12: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
8P GAIN MUTATED 4 0 2 3
8P GAIN WILD-TYPE 62 54 16 21

Figure S9.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.22

Table S10.  Gene #18: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
11P GAIN MUTATED 1 0 2 2 0
11P GAIN WILD-TYPE 36 40 8 48 25

Figure S10.  Get High-res Image Gene #18: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00513 (Fisher's exact test), Q value = 0.059

Table S11.  Gene #19: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
12P GAIN MUTATED 3 1 7
12P GAIN WILD-TYPE 37 76 38

Figure S11.  Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.13

Table S12.  Gene #19: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
12P GAIN MUTATED 9 1 1
12P GAIN WILD-TYPE 54 43 54

Figure S12.  Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.11

Table S13.  Gene #19: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
12P GAIN MUTATED 2 2 0 7 0
12P GAIN WILD-TYPE 31 48 16 26 29

Figure S13.  Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.19

Table S14.  Gene #19: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
12P GAIN MUTATED 3 1 1 0 5 0 1
12P GAIN WILD-TYPE 15 40 26 15 18 18 18

Figure S14.  Get High-res Image Gene #19: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.21

Table S15.  Gene #20: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
12Q GAIN MUTATED 10 1 3
12Q GAIN WILD-TYPE 53 43 52

Figure S15.  Get High-res Image Gene #20: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.22

Table S16.  Gene #21: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
13Q GAIN MUTATED 0 6 0 3 0
13Q GAIN WILD-TYPE 37 34 10 47 25

Figure S16.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00885 (Fisher's exact test), Q value = 0.092

Table S17.  Gene #21: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
13Q GAIN MUTATED 2 0 6 1
13Q GAIN WILD-TYPE 30 65 38 20

Figure S17.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00911 (Fisher's exact test), Q value = 0.094

Table S18.  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 S18.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.16

Table S19.  Gene #21: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
13Q GAIN MUTATED 7 2 0
13Q GAIN WILD-TYPE 56 42 55

Figure S19.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0077 (Fisher's exact test), Q value = 0.084

Table S20.  Gene #21: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
13Q GAIN MUTATED 2 0 0 6 1
13Q GAIN WILD-TYPE 31 50 16 27 28

Figure S20.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00474 (Fisher's exact test), Q value = 0.056

Table S21.  Gene #21: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
13Q GAIN MUTATED 2 0 0 0 5 1 1
13Q GAIN WILD-TYPE 16 41 27 15 18 17 18

Figure S21.  Get High-res Image Gene #21: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.22

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'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.21

Table S23.  Gene #30: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
19Q GAIN MUTATED 3 3 8
19Q GAIN WILD-TYPE 37 74 37

Figure S23.  Get High-res Image Gene #30: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.21

Table S24.  Gene #32: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
20Q GAIN MUTATED 8 1 1
20Q GAIN WILD-TYPE 55 43 54

Figure S24.  Get High-res Image Gene #32: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.22

Table S25.  Gene #34: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
22Q GAIN MUTATED 0 0 0 3 0
22Q GAIN WILD-TYPE 33 50 16 30 29

Figure S25.  Get High-res Image Gene #34: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.13

Table S26.  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 S26.  Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.19

Table S27.  Gene #35: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
XP GAIN MUTATED 4 0 1 1 0
XP GAIN WILD-TYPE 29 50 15 32 29

Figure S27.  Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.13

Table S28.  Gene #35: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
XP GAIN MUTATED 3 0 1 0 0 2 0
XP GAIN WILD-TYPE 15 41 26 15 23 16 19

Figure S28.  Get High-res Image Gene #35: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.16

Table S29.  Gene #36: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
XQ GAIN MUTATED 4 0 0 1 0
XQ GAIN WILD-TYPE 29 50 16 32 29

Figure S29.  Get High-res Image Gene #36: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.034

Table S30.  Gene #36: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
XQ GAIN MUTATED 3 0 0 0 0 2 0
XQ GAIN WILD-TYPE 15 41 27 15 23 16 19

Figure S30.  Get High-res Image Gene #36: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

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

Table S31.  Gene #37: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
1P LOSS MUTATED 27 12 6 30 22
1P LOSS WILD-TYPE 10 28 4 20 3

Figure S31.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.048

Table S32.  Gene #37: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
1P LOSS MUTATED 17 56 24
1P LOSS WILD-TYPE 23 21 21

Figure S32.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0022

Table S33.  Gene #37: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
1P LOSS MUTATED 10 17 16
1P LOSS WILD-TYPE 21 1 12

Figure S33.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 0.08

Table S34.  Gene #37: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
1P LOSS MUTATED 20 48 19 10
1P LOSS WILD-TYPE 12 17 25 11

Figure S34.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00378 (Fisher's exact test), Q value = 0.048

Table S35.  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 49 23 10
1P LOSS WILD-TYPE 19 15 20 11

Figure S35.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0089

Table S36.  Gene #37: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
1P LOSS MUTATED 28 25 44
1P LOSS WILD-TYPE 35 19 11

Figure S36.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.18

Table S37.  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 40 11 15
1P LOSS WILD-TYPE 35 14 7 9

Figure S37.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.012

Table S38.  Gene #37: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
1P LOSS MUTATED 16 41 11 13 16
1P LOSS WILD-TYPE 17 9 5 20 13

Figure S38.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.038

Table S39.  Gene #37: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
1P LOSS MUTATED 7 33 16 12 8 11 10
1P LOSS WILD-TYPE 11 8 11 3 15 7 9

Figure S39.  Get High-res Image Gene #37: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.24

Table S40.  Gene #38: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
1Q LOSS MUTATED 1 2 7
1Q LOSS WILD-TYPE 30 16 21

Figure S40.  Get High-res Image Gene #38: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.057

Table S41.  Gene #39: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
2P LOSS MUTATED 0 1 7 2
2P LOSS WILD-TYPE 32 64 37 19

Figure S41.  Get High-res Image Gene #39: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.012

Table S42.  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 S42.  Get High-res Image Gene #39: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.11

Table S43.  Gene #39: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
2P LOSS MUTATED 1 1 0 0 2 5 1
2P LOSS WILD-TYPE 17 40 27 15 21 13 18

Figure S43.  Get High-res Image Gene #39: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.13

Table S44.  Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
3P LOSS MUTATED 11 13 1 28 7
3P LOSS WILD-TYPE 26 27 9 22 18

Figure S44.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0091

Table S45.  Gene #41: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
3P LOSS MUTATED 16 16 25 3
3P LOSS WILD-TYPE 16 49 19 18

Figure S45.  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 = 0.001

Table S46.  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 18 30 3
3P LOSS WILD-TYPE 25 46 13 18

Figure S46.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

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

Table S47.  Gene #41: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
3P LOSS MUTATED 34 8 18
3P LOSS WILD-TYPE 29 36 37

Figure S47.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.048

Table S48.  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 35 16 5 4
3P LOSS WILD-TYPE 31 38 13 20

Figure S48.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.014

Table S49.  Gene #41: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
3P LOSS MUTATED 10 16 3 23 8
3P LOSS WILD-TYPE 23 34 13 10 21

Figure S49.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S50.  Gene #41: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
3P LOSS MUTATED 4 15 13 1 19 5 3
3P LOSS WILD-TYPE 14 26 14 14 4 13 16

Figure S50.  Get High-res Image Gene #41: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.001

Table S51.  Gene #42: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
3Q LOSS MUTATED 9 12 6 40 20
3Q LOSS WILD-TYPE 28 28 4 10 5

Figure S51.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.18

Table S52.  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 S52.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.001

Table S53.  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 41 33 7
3Q LOSS WILD-TYPE 28 23 10 14

Figure S53.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

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

Table S54.  Gene #42: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
3Q LOSS MUTATED 38 13 36
3Q LOSS WILD-TYPE 25 31 19

Figure S54.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.24

Table S55.  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 33 5 10
3Q LOSS WILD-TYPE 27 21 13 14

Figure S55.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.048

Table S56.  Gene #42: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
3Q LOSS MUTATED 10 33 6 23 15
3Q LOSS WILD-TYPE 23 17 10 10 14

Figure S56.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S57.  Gene #42: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
3Q LOSS MUTATED 5 28 16 7 19 5 7
3Q LOSS WILD-TYPE 13 13 11 8 4 13 12

Figure S57.  Get High-res Image Gene #42: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.056

Table S58.  Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
4P LOSS MUTATED 0 8 0 3 0
4P LOSS WILD-TYPE 37 32 10 47 25

Figure S58.  Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00781 (Fisher's exact test), Q value = 0.084

Table S59.  Gene #43: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
4P LOSS MUTATED 0 3 8 0
4P LOSS WILD-TYPE 32 62 36 21

Figure S59.  Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.19

Table S60.  Gene #43: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
4P LOSS MUTATED 0 2 1 1 6 1 0
4P LOSS WILD-TYPE 18 39 26 14 17 17 19

Figure S60.  Get High-res Image Gene #43: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.15

Table S61.  Gene #44: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
4Q LOSS MUTATED 0 3 7 0
4Q LOSS WILD-TYPE 32 62 37 21

Figure S61.  Get High-res Image Gene #44: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.22

Table S62.  Gene #45: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
5P LOSS MUTATED 1 0 4 0
5P LOSS WILD-TYPE 31 65 40 21

Figure S62.  Get High-res Image Gene #45: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.22

Table S63.  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 S63.  Get High-res Image Gene #45: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.011

Table S64.  Gene #47: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
6Q LOSS MUTATED 1 0 3 11 3
6Q LOSS WILD-TYPE 36 40 7 39 22

Figure S64.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.011

Table S65.  Gene #47: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
6Q LOSS MUTATED 0 16 2
6Q LOSS WILD-TYPE 40 61 43

Figure S65.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.22

Table S66.  Gene #47: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 23 18
6Q LOSS MUTATED 2 2 7 0
6Q LOSS WILD-TYPE 14 18 16 18

Figure S66.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.023

Table S67.  Gene #47: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
6Q LOSS MUTATED 1 15 1 1
6Q LOSS WILD-TYPE 31 50 43 20

Figure S67.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.0026

Table S68.  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 16 1 1
6Q LOSS WILD-TYPE 34 48 42 20

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

'6q loss' versus 'MIRSEQ_CNMF'

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

Table S69.  Gene #47: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
6Q LOSS MUTATED 1 4 13
6Q LOSS WILD-TYPE 62 40 42

Figure S69.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0022

Table S70.  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 15 1 1
6Q LOSS WILD-TYPE 65 39 17 23

Figure S70.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.019

Table S71.  Gene #47: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
6Q LOSS MUTATED 0 11 0 4 1 1 1
6Q LOSS WILD-TYPE 18 30 27 11 22 17 18

Figure S71.  Get High-res Image Gene #47: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.17

Table S72.  Gene #48: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
7Q LOSS MUTATED 0 7 0 0
7Q LOSS WILD-TYPE 32 58 44 21

Figure S72.  Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.19

Table S73.  Gene #48: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
7Q LOSS MUTATED 0 2 5
7Q LOSS WILD-TYPE 63 42 50

Figure S73.  Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.11

Table S74.  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 2 0
7Q LOSS WILD-TYPE 66 49 16 24

Figure S74.  Get High-res Image Gene #48: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'RPPA_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.13

Table S75.  Gene #51: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 23 18
9P LOSS MUTATED 0 0 4 0
9P LOSS WILD-TYPE 16 20 19 18

Figure S75.  Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.15

Table S76.  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 S76.  Get High-res Image Gene #51: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.16

Table S77.  Gene #53: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
11P LOSS MUTATED 10 20 0 15 9
11P LOSS WILD-TYPE 27 20 10 35 16

Figure S77.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0096

Table S78.  Gene #53: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
11P LOSS MUTATED 20 14 20
11P LOSS WILD-TYPE 20 63 25

Figure S78.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.012

Table S79.  Gene #53: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
11P LOSS MUTATED 11 12 25 6
11P LOSS WILD-TYPE 21 53 19 15

Figure S79.  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 = 0.001

Table S80.  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 S80.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0022

Table S81.  Gene #53: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
11P LOSS MUTATED 34 11 9
11P LOSS WILD-TYPE 29 33 46

Figure S81.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.001

Table S82.  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 S82.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0073

Table S83.  Gene #53: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
11P LOSS MUTATED 11 6 4 19 13
11P LOSS WILD-TYPE 22 44 12 14 16

Figure S83.  Get High-res Image Gene #53: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.001

Table S84.  Gene #53: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
11P LOSS MUTATED 9 5 9 2 18 5 5
11P LOSS WILD-TYPE 9 36 18 13 5 13 14

Figure S84.  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 S85.  Gene #54: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
11Q LOSS MUTATED 6 19 0 15 0
11Q LOSS WILD-TYPE 31 21 10 35 25

Figure S85.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.19

Table S86.  Gene #54: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
11Q LOSS MUTATED 14 12 14
11Q LOSS WILD-TYPE 26 65 31

Figure S86.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.012

Table S87.  Gene #54: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
11Q LOSS MUTATED 7 8 21 4
11Q LOSS WILD-TYPE 25 57 23 17

Figure S87.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S88.  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 S88.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0022

Table S89.  Gene #54: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
11Q LOSS MUTATED 26 10 4
11Q LOSS WILD-TYPE 37 34 51

Figure S89.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.01

Table S90.  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 S90.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.01

Table S91.  Gene #54: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
11Q LOSS MUTATED 8 4 3 17 8
11Q LOSS WILD-TYPE 25 46 13 16 21

Figure S91.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0019

Table S92.  Gene #54: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
11Q LOSS MUTATED 7 5 6 1 15 2 4
11Q LOSS WILD-TYPE 11 36 21 14 8 16 15

Figure S92.  Get High-res Image Gene #54: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.19

Table S93.  Gene #55: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
12P LOSS MUTATED 2 0 1 0 0
12P LOSS WILD-TYPE 35 40 9 50 25

Figure S93.  Get High-res Image Gene #55: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.024

Table S94.  Gene #57: '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 S94.  Get High-res Image Gene #57: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.012

Table S95.  Gene #57: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
14Q LOSS MUTATED 1 6 0 0 4 8 1
14Q LOSS WILD-TYPE 17 35 27 15 19 10 18

Figure S95.  Get High-res Image Gene #57: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.19

Table S96.  Gene #60: '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 S96.  Get High-res Image Gene #60: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.015

Table S97.  Gene #61: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
17P LOSS MUTATED 12 12 8 26 4
17P LOSS WILD-TYPE 25 28 2 24 21

Figure S97.  Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.032

Table S98.  Gene #61: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
17P LOSS MUTATED 9 40 13
17P LOSS WILD-TYPE 31 37 32

Figure S98.  Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.19

Table S99.  Gene #61: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
17P LOSS MUTATED 9 34 14 5
17P LOSS WILD-TYPE 23 31 30 16

Figure S99.  Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.16

Table S100.  Gene #61: '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 34 13 5
17P LOSS WILD-TYPE 24 30 30 16

Figure S100.  Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.18

Table S101.  Gene #61: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
17P LOSS MUTATED 20 13 29
17P LOSS WILD-TYPE 43 31 26

Figure S101.  Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.15

Table S102.  Gene #61: '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 8 7
17P LOSS WILD-TYPE 48 25 10 17

Figure S102.  Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.22

Table S103.  Gene #61: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
17P LOSS MUTATED 8 20 4 9 8 8 5
17P LOSS WILD-TYPE 10 21 23 6 15 10 14

Figure S103.  Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.19

Table S104.  Gene #63: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
18P LOSS MUTATED 0 5 3 5 3
18P LOSS WILD-TYPE 37 35 7 45 22

Figure S104.  Get High-res Image Gene #63: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.22

Table S105.  Gene #65: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
19Q LOSS MUTATED 1 0 1 0 3
19Q LOSS WILD-TYPE 32 50 15 33 26

Figure S105.  Get High-res Image Gene #65: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.15

Table S106.  Gene #67: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
21Q LOSS MUTATED 3 19 14
21Q LOSS WILD-TYPE 37 58 31

Figure S106.  Get High-res Image Gene #67: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.001

Table S107.  Gene #68: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
22Q LOSS MUTATED 15 4 9 27 3
22Q LOSS WILD-TYPE 22 36 1 23 22

Figure S107.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.16

Table S108.  Gene #68: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
22Q LOSS MUTATED 9 36 13
22Q LOSS WILD-TYPE 31 41 32

Figure S108.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.15

Table S109.  Gene #68: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
22Q LOSS MUTATED 8 32 10 8
22Q LOSS WILD-TYPE 24 33 34 13

Figure S109.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.031

Table S110.  Gene #68: '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 S110.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.2

Table S111.  Gene #68: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
22Q LOSS MUTATED 15 18 25
22Q LOSS WILD-TYPE 48 26 30

Figure S111.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.21

Table S112.  Gene #68: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 50 16 33 29
22Q LOSS MUTATED 9 26 7 7 9
22Q LOSS WILD-TYPE 24 24 9 26 20

Figure S112.  Get High-res Image Gene #68: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0059

Table S113.  Gene #69: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
XP LOSS MUTATED 7 4 2 25 10
XP LOSS WILD-TYPE 30 36 8 25 15

Figure S113.  Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0023

Table S114.  Gene #69: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
XP LOSS MUTATED 10 34 4
XP LOSS WILD-TYPE 30 43 41

Figure S114.  Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.22

Table S115.  Gene #69: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 23 18
XP LOSS MUTATED 7 8 8 1
XP LOSS WILD-TYPE 9 12 15 17

Figure S115.  Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.13

Table S116.  Gene #69: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
XP LOSS MUTATED 10 27 9 2
XP LOSS WILD-TYPE 22 38 35 19

Figure S116.  Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.018

Table S117.  Gene #69: '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 S117.  Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.013

Table S118.  Gene #69: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
XP LOSS MUTATED 12 9 27
XP LOSS WILD-TYPE 51 35 28

Figure S118.  Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.15

Table S119.  Gene #69: '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 S119.  Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00839 (Fisher's exact test), Q value = 0.089

Table S120.  Gene #69: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
XP LOSS MUTATED 3 20 6 6 5 7 1
XP LOSS WILD-TYPE 15 21 21 9 18 11 18

Figure S120.  Get High-res Image Gene #69: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0023

Table S121.  Gene #70: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
XQ LOSS MUTATED 7 4 2 26 10
XQ LOSS WILD-TYPE 30 36 8 24 15

Figure S121.  Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0022

Table S122.  Gene #70: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 77 45
XQ LOSS MUTATED 10 35 4
XQ LOSS WILD-TYPE 30 42 41

Figure S122.  Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.18

Table S123.  Gene #70: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 23 18
XQ LOSS MUTATED 7 9 8 1
XQ LOSS WILD-TYPE 9 11 15 17

Figure S123.  Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00932 (Fisher's exact test), Q value = 0.095

Table S124.  Gene #70: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 65 44 21
XQ LOSS MUTATED 10 28 9 2
XQ LOSS WILD-TYPE 22 37 35 19

Figure S124.  Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.012

Table S125.  Gene #70: '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 S125.  Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.019

Table S126.  Gene #70: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 44 55
XQ LOSS MUTATED 12 10 27
XQ LOSS WILD-TYPE 51 34 28

Figure S126.  Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.1

Table S127.  Gene #70: '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 S127.  Get High-res Image Gene #70: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00415 (Fisher's exact test), Q value = 0.051

Table S128.  Gene #70: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 41 27 15 23 18 19
XQ LOSS MUTATED 3 21 6 6 5 7 1
XQ LOSS WILD-TYPE 15 20 21 9 18 11 18

Figure S128.  Get High-res Image Gene #70: '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/22533878/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/22542422/PCPG-TP.transferedmergedcluster.txt

  • Number of patients = 162

  • Number of significantly arm-level cnvs = 70

  • 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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