Correlation between copy number variations of arm-level result and molecular subtypes
Skin Cutaneous Melanoma (Metastatic)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C18P5ZKJ
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/C18P5ZKJ
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 366 patients, 172 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 3p gain cnv correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

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

  • 12q gain cnv correlated to 'CN_CNMF'.

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

  • 15q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 17q gain cnv correlated to 'METHLYATION_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 21q gain cnv correlated to 'METHLYATION_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

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

  • xq gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 2p loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 2q loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

  • 6p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 7q loss cnv correlated to 'METHLYATION_CNMF'.

  • 8p loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • 9q loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

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

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

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 13q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 16q loss cnv correlated to 'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'METHLYATION_CNMF'.

  • 18p loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

  • 19p loss cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 20p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 172 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
2p gain 67 (18%) 299 0.0114
(0.0926) 		0.261
(0.568) 		0.801
(0.931) 		0.815
(0.942) 		0.00403
(0.0486) 		0.00772
(0.0749) 		0.105
(0.347) 		0.00012
(0.00444) 		0.039
(0.204) 		0.0286
(0.169)
6p gain 144 (39%) 222 0.00043
(0.0101) 		6e-05
(0.00273) 		0.988
(1.00) 		0.144
(0.42) 		0.322
(0.633) 		0.0247
(0.152) 		0.00214
(0.0303) 		0.0566
(0.249) 		0.00028
(0.00741) 		0.0018
(0.0268)
11p gain 35 (10%) 331 0.00609
(0.0636) 		0.0945
(0.327) 		0.0846
(0.304) 		0.189
(0.487) 		0.0013
(0.0219) 		0.00777
(0.0749) 		0.0233
(0.147) 		0.00628
(0.0636) 		0.231
(0.529) 		0.0174
(0.118)
11q gain 29 (8%) 337 0.0002
(0.00607) 		0.19
(0.487) 		0.0764
(0.285) 		0.0849
(0.304) 		0.00306
(0.0392) 		0.00131
(0.0219) 		0.00598
(0.0636) 		0.00075
(0.0152) 		0.0574
(0.25) 		0.0136
(0.102)
6p loss 68 (19%) 298 0.00504
(0.0579) 		0.468
(0.74) 		0.873
(0.969) 		0.277
(0.582) 		0.0126
(0.0977) 		0.0352
(0.189) 		0.0419
(0.214) 		0.0895
(0.316) 		0.0258
(0.157) 		0.0275
(0.164)
xp loss 97 (27%) 269 0.0307
(0.178) 		1e-05
(0.000586) 		0.0865
(0.309) 		0.226
(0.523) 		0.00109
(0.0199) 		0.00396
(0.0485) 		0.0247
(0.152) 		0.339
(0.639) 		0.0309
(0.178) 		0.752
(0.908)
2q gain 65 (18%) 301 0.00794
(0.0749) 		0.45
(0.727) 		0.777
(0.918) 		0.342
(0.644) 		0.00051
(0.0113) 		0.0116
(0.0926) 		0.138
(0.409) 		7e-05
(0.00302) 		0.0528
(0.246) 		0.00212
(0.0303)
xq loss 93 (25%) 273 0.0395
(0.205) 		1e-05
(0.000586) 		0.241
(0.541) 		0.0784
(0.287) 		0.0007
(0.0147) 		0.00625
(0.0636) 		0.0698
(0.274) 		0.717
(0.883) 		0.0353
(0.189) 		0.75
(0.908)
13q gain 94 (26%) 272 1e-05
(0.000586) 		1e-05
(0.000586) 		0.459
(0.736) 		0.314
(0.628) 		0.00047
(0.0107) 		0.00626
(0.0636) 		0.499
(0.753) 		0.839
(0.957) 		0.0907
(0.319) 		0.685
(0.862)
20p gain 147 (40%) 219 1e-05
(0.000586) 		0.009
(0.0809) 		0.843
(0.957) 		0.984
(1.00) 		0.00015
(0.00492) 		0.0208
(0.134) 		0.487
(0.753) 		0.271
(0.578) 		0.273
(0.579) 		0.0659
(0.264)
xp gain 41 (11%) 325 0.00013
(0.00444) 		0.00161
(0.0254) 		0.958
(0.999) 		0.228
(0.527) 		0.00728
(0.0728) 		0.22
(0.519) 		0.664
(0.846) 		0.398
(0.684) 		0.00109
(0.0199) 		0.406
(0.69)
xq gain 43 (12%) 323 8e-05
(0.00328) 		0.00031
(0.00794) 		0.585
(0.789) 		0.986
(1.00) 		0.00446
(0.0522) 		0.188
(0.487) 		0.387
(0.675) 		0.277
(0.582) 		0.00023
(0.00674) 		0.756
(0.909)
1p loss 53 (14%) 313 0.0479
(0.23) 		0.00026
(0.00711) 		0.587
(0.79) 		0.315
(0.628) 		0.0107
(0.0904) 		0.134
(0.402) 		0.00933
(0.0814) 		0.693
(0.865) 		0.179
(0.476) 		0.0544
(0.246)
2p loss 51 (14%) 315 0.373
(0.662) 		0.212
(0.514) 		0.0457
(0.228) 		0.0149
(0.107) 		0.927
(0.989) 		0.0353
(0.189) 		0.00306
(0.0392) 		0.0655
(0.264) 		0.224
(0.521) 		0.212
(0.514)
10q loss 224 (61%) 142 1e-05
(0.000586) 		0.208
(0.508) 		0.921
(0.989) 		0.202
(0.501) 		0.00019
(0.00599) 		0.00239
(0.0332) 		0.0209
(0.134) 		0.363
(0.653) 		0.33
(0.636) 		0.501
(0.753)
14q loss 112 (31%) 254 1e-05
(0.000586) 		0.32
(0.632) 		0.41
(0.692) 		0.271
(0.578) 		0.00907
(0.0809) 		0.0331
(0.186) 		0.00571
(0.0624) 		0.216
(0.519) 		0.334
(0.636) 		0.236
(0.535)
1q gain 171 (47%) 195 1e-05
(0.000586) 		0.664
(0.846) 		0.271
(0.578) 		0.51
(0.758) 		0.0335
(0.186) 		0.333
(0.636) 		0.125
(0.392) 		0.319
(0.631) 		0.0478
(0.23) 		0.286
(0.595)
3q gain 72 (20%) 294 0.564
(0.778) 		0.463
(0.738) 		0.0184
(0.122) 		0.046
(0.228) 		0.0462
(0.228) 		0.239
(0.541) 		0.132
(0.402) 		0.533
(0.762) 		0.201
(0.5) 		0.617
(0.815)
7q gain 200 (55%) 166 3e-05
(0.00154) 		0.912
(0.984) 		0.692
(0.865) 		0.515
(0.758) 		0.00593
(0.0636) 		0.19
(0.487) 		0.686
(0.862) 		0.57
(0.78) 		0.00865
(0.0797) 		0.3
(0.612)
8p gain 121 (33%) 245 1e-05
(0.000586) 		0.177
(0.473) 		0.613
(0.813) 		0.844
(0.957) 		0.0131
(0.0995) 		0.0355
(0.189) 		0.524
(0.76) 		0.843
(0.957) 		0.852
(0.964) 		0.437
(0.713)
8q gain 169 (46%) 197 1e-05
(0.000586) 		0.00112
(0.02) 		0.694
(0.865) 		0.796
(0.93) 		0.00411
(0.0488) 		0.112
(0.364) 		0.63
(0.827) 		0.892
(0.974) 		0.808
(0.937) 		0.376
(0.662)
15q gain 85 (23%) 281 5e-05
(0.00241) 		0.195
(0.493) 		0.945
(0.989) 		0.818
(0.944) 		0.00372
(0.0469) 		0.0161
(0.113) 		0.193
(0.493) 		0.173
(0.463) 		0.376
(0.662) 		0.0573
(0.25)
16p gain 58 (16%) 308 0.00161
(0.0254) 		0.0342
(0.187) 		0.988
(1.00) 		0.657
(0.845) 		0.00036
(0.00895) 		0.123
(0.39) 		0.785
(0.924) 		0.0751
(0.282) 		0.07
(0.274) 		0.123
(0.39)
16q gain 44 (12%) 322 0.00026
(0.00711) 		0.0535
(0.246) 		0.275
(0.581) 		0.627
(0.823) 		2e-05
(0.00109) 		0.0332
(0.186) 		0.787
(0.924) 		0.0993
(0.336) 		0.055
(0.246) 		0.147
(0.425)
19p gain 57 (16%) 309 0.00508
(0.0579) 		0.0236
(0.148) 		0.253
(0.559) 		0.798
(0.93) 		0.00135
(0.0221) 		0.24
(0.541) 		0.906
(0.981) 		0.543
(0.77) 		0.172
(0.463) 		0.901
(0.981)
19q gain 56 (15%) 310 0.0106
(0.0904) 		0.0178
(0.12) 		0.295
(0.606) 		1
(1.00) 		0.00012
(0.00444) 		0.0622
(0.255) 		0.527
(0.76) 		0.432
(0.712) 		0.155
(0.44) 		0.855
(0.964)
20q gain 179 (49%) 187 1e-05
(0.000586) 		0.0165
(0.114) 		0.941
(0.989) 		0.974
(1.00) 		0.00384
(0.0477) 		0.163
(0.451) 		0.479
(0.746) 		0.26
(0.568) 		0.915
(0.985) 		0.28
(0.586)
2q loss 52 (14%) 314 0.815
(0.942) 		0.196
(0.495) 		0.0111
(0.091) 		0.0017
(0.0258) 		0.759
(0.911) 		0.214
(0.517) 		0.00793
(0.0749) 		0.118
(0.381) 		0.167
(0.454) 		0.223
(0.52)
6q loss 172 (47%) 194 1e-05
(0.000586) 		0.0142
(0.105) 		0.978
(1.00) 		0.482
(0.748) 		0.00249
(0.034) 		0.0814
(0.297) 		0.221
(0.519) 		0.219
(0.519) 		0.403
(0.687) 		0.162
(0.451)
10p loss 204 (56%) 162 1e-05
(0.000586) 		0.129
(0.4) 		0.924
(0.989) 		0.411
(0.692) 		0.00117
(0.0204) 		0.0161
(0.113) 		0.0608
(0.255) 		0.35
(0.651) 		0.372
(0.662) 		0.564
(0.778)
16q loss 106 (29%) 260 0.302
(0.614) 		0.325
(0.636) 		0.0154
(0.11) 		0.755
(0.909) 		0.0372
(0.196) 		0.0357
(0.189) 		0.328
(0.636) 		0.104
(0.347) 		0.0682
(0.27) 		0.182
(0.478)
3p gain 63 (17%) 303 0.22
(0.519) 		0.251
(0.557) 		0.0445
(0.225) 		0.0199
(0.129) 		0.417
(0.699) 		0.33
(0.636) 		0.331
(0.636) 		0.555
(0.775) 		0.755
(0.909) 		0.975
(1.00)
4p gain 56 (15%) 310 0.00167
(0.0258) 		0.189
(0.487) 		0.305
(0.617) 		0.857
(0.964) 		0.315
(0.628) 		0.247
(0.549) 		0.305
(0.617) 		0.0458
(0.228) 		0.73
(0.896) 		0.562
(0.778)
4q gain 47 (13%) 319 0.0115
(0.0926) 		0.321
(0.632) 		0.263
(0.57) 		0.934
(0.989) 		0.213
(0.516) 		0.387
(0.675) 		0.687
(0.862) 		0.0421
(0.214) 		0.774
(0.917) 		0.942
(0.989)
7p gain 203 (55%) 163 1e-05
(0.000586) 		0.937
(0.989) 		0.459
(0.736) 		0.374
(0.662) 		0.0189
(0.124) 		0.199
(0.5) 		0.0749
(0.282) 		0.741
(0.902) 		0.173
(0.463) 		0.57
(0.78)
12p gain 65 (18%) 301 0.00078
(0.0152) 		0.164
(0.451) 		0.54
(0.768) 		0.426
(0.705) 		0.0123
(0.0961) 		0.864
(0.967) 		0.873
(0.969) 		0.493
(0.753) 		0.166
(0.454) 		0.37
(0.662)
17p gain 37 (10%) 329 0.00908
(0.0809) 		0.00102
(0.0195) 		0.579
(0.786) 		0.532
(0.762) 		0.0784
(0.287) 		0.512
(0.758) 		0.572
(0.78) 		0.293
(0.606) 		0.975
(1.00) 		0.139
(0.409)
4q loss 85 (23%) 281 0.529
(0.76) 		0.0702
(0.274) 		0.481
(0.747) 		0.751
(0.908) 		0.217
(0.519) 		0.0328
(0.186) 		0.903
(0.981) 		0.00559
(0.0619) 		0.605
(0.808) 		0.243
(0.543)
8q loss 27 (7%) 339 0.52
(0.759) 		0.00795
(0.0749) 		0.316
(0.628) 		0.535
(0.764) 		0.231
(0.529) 		0.738
(0.902) 		0.409
(0.692) 		0.504
(0.757) 		0.0147
(0.107) 		0.146
(0.423)
9p loss 236 (64%) 130 0.00013
(0.00444) 		0.133
(0.402) 		0.644
(0.838) 		0.451
(0.727) 		0.00275
(0.0364) 		0.101
(0.34) 		0.0753
(0.282) 		0.221
(0.519) 		0.739
(0.902) 		0.591
(0.793)
9q loss 185 (51%) 181 0.272
(0.579) 		0.0709
(0.275) 		0.992
(1.00) 		0.149
(0.43) 		0.0122
(0.0961) 		0.334
(0.636) 		0.0398
(0.205) 		0.138
(0.409) 		0.969
(1.00) 		0.466
(0.739)
11q loss 148 (40%) 218 0.013
(0.0995) 		0.35
(0.651) 		0.952
(0.994) 		0.696
(0.866) 		0.222
(0.519) 		0.00195
(0.0286) 		0.736
(0.901) 		0.158
(0.446) 		0.0752
(0.282) 		0.55
(0.775)
12q loss 67 (18%) 299 0.0333
(0.186) 		0.00806
(0.0751) 		0.983
(1.00) 		0.876
(0.97) 		0.0503
(0.237) 		0.557
(0.775) 		0.133
(0.402) 		0.501
(0.753) 		0.451
(0.727) 		0.698
(0.866)
13q loss 80 (22%) 286 0.935
(0.989) 		0.0111
(0.091) 		0.0656
(0.264) 		0.557
(0.775) 		0.661
(0.846) 		0.0342
(0.187) 		0.797
(0.93) 		0.203
(0.503) 		0.323
(0.633) 		0.472
(0.741)
18p loss 104 (28%) 262 0.732
(0.897) 		0.601
(0.804) 		0.377
(0.662) 		0.51
(0.758) 		0.0261
(0.157) 		0.164
(0.451) 		0.0275
(0.164) 		0.39
(0.677) 		0.545
(0.77) 		0.152
(0.436)
19q loss 73 (20%) 293 0.0249
(0.153) 		0.0472
(0.23) 		0.977
(1.00) 		0.0822
(0.298) 		0.0918
(0.32) 		0.494
(0.753) 		0.488
(0.753) 		0.989
(1.00) 		0.0539
(0.246) 		0.527
(0.76)
20p loss 26 (7%) 340 0.371
(0.662) 		0.62
(0.818) 		0.236
(0.535) 		0.772
(0.917) 		0.2
(0.5) 		0.0216
(0.137) 		0.134
(0.402) 		0.0167
(0.114) 		0.891
(0.974) 		0.188
(0.487)
5p gain 76 (21%) 290 0.00062
(0.0134) 		0.172
(0.463) 		0.889
(0.974) 		0.397
(0.684) 		0.222
(0.519) 		0.58
(0.786) 		0.0879
(0.312) 		0.498
(0.753) 		0.985
(1.00) 		0.0958
(0.329)
5q gain 52 (14%) 314 0.0108
(0.0904) 		0.139
(0.41) 		0.357
(0.651) 		0.139
(0.409) 		0.982
(1.00) 		0.775
(0.917) 		0.105
(0.347) 		0.522
(0.759) 		0.33
(0.636) 		0.0732
(0.282)
12q gain 39 (11%) 327 0.0164
(0.114) 		1
(1.00) 		0.616
(0.815) 		0.0579
(0.25) 		0.539
(0.768) 		0.646
(0.838) 		0.817
(0.944) 		0.0612
(0.255) 		0.423
(0.7) 		0.68
(0.861)
17q gain 65 (18%) 301 0.0507
(0.237) 		0.0478
(0.23) 		0.103
(0.344) 		0.276
(0.581) 		0.985
(1.00) 		0.334
(0.636) 		0.48
(0.747) 		0.673
(0.855) 		0.556
(0.775) 		0.762
(0.913)
18p gain 55 (15%) 311 0.00255
(0.0343) 		0.606
(0.808) 		0.208
(0.508) 		0.39
(0.677) 		0.26
(0.568) 		0.664
(0.846) 		0.933
(0.989) 		0.966
(1.00) 		0.0609
(0.255) 		0.473
(0.741)
18q gain 44 (12%) 322 0.00077
(0.0152) 		0.677
(0.858) 		0.35
(0.651) 		0.47
(0.74) 		0.217
(0.519) 		0.83
(0.953) 		0.674
(0.855) 		0.764
(0.914) 		0.644
(0.838) 		0.797
(0.93)
21q gain 67 (18%) 299 0.164
(0.451) 		0.0483
(0.23) 		0.888
(0.974) 		0.529
(0.76) 		0.194
(0.493) 		0.357
(0.651) 		0.109
(0.356) 		0.997
(1.00) 		0.949
(0.993) 		0.512
(0.758)
22q gain 126 (34%) 240 0.00038
(0.00916) 		0.118
(0.381) 		0.894
(0.975) 		0.945
(0.989) 		0.074
(0.282) 		0.252
(0.559) 		0.617
(0.815) 		0.159
(0.447) 		0.698
(0.866) 		0.496
(0.753)
3q loss 53 (14%) 313 0.0464
(0.228) 		0.091
(0.319) 		0.509
(0.758) 		0.372
(0.662) 		0.375
(0.662) 		0.254
(0.56) 		0.129
(0.4) 		0.633
(0.83) 		0.328
(0.636) 		0.771
(0.917)
4p loss 80 (22%) 286 0.529
(0.76) 		0.2
(0.5) 		0.352
(0.651) 		0.969
(1.00) 		0.163
(0.451) 		0.0661
(0.264) 		0.543
(0.77) 		0.0132
(0.0995) 		0.879
(0.971) 		0.316
(0.628)
7q loss 17 (5%) 349 0.359
(0.652) 		0.0105
(0.0904) 		0.337
(0.637) 		0.437
(0.713) 		0.404
(0.687) 		0.418
(0.699) 		0.521
(0.759) 		0.772
(0.917) 		0.0962
(0.329) 		0.928
(0.989)
8p loss 67 (18%) 299 0.122
(0.39) 		0.451
(0.727) 		0.0587
(0.252) 		0.296
(0.606) 		0.0578
(0.25) 		0.525
(0.76) 		0.462
(0.737) 		0.0293
(0.172) 		0.436
(0.713) 		0.181
(0.476)
11p loss 126 (34%) 240 0.0179
(0.12) 		0.0559
(0.248) 		0.584
(0.789) 		0.294
(0.606) 		0.469
(0.74) 		0.098
(0.334) 		0.522
(0.759) 		0.335
(0.637) 		0.0834
(0.301) 		0.569
(0.78)
12p loss 59 (16%) 307 0.22
(0.519) 		0.106
(0.349) 		0.857
(0.964) 		0.872
(0.969) 		0.0144
(0.106) 		0.892
(0.974) 		0.125
(0.392) 		0.435
(0.713) 		0.981
(1.00) 		0.577
(0.786)
17p loss 127 (35%) 239 0.0784
(0.287) 		0.00551
(0.0619) 		0.444
(0.722) 		0.515
(0.758) 		0.187
(0.487) 		0.0532
(0.246) 		0.88
(0.971) 		0.519
(0.759) 		0.624
(0.822) 		0.442
(0.721)
19p loss 77 (21%) 289 0.0749
(0.282) 		0.658
(0.845) 		0.783
(0.923) 		0.0335
(0.186) 		0.147
(0.425) 		0.256
(0.562) 		0.567
(0.779) 		0.887
(0.974) 		0.236
(0.535) 		0.516
(0.758)
20q loss 9 (2%) 357 0.398
(0.684) 		0.18
(0.476) 		0.0738
(0.282) 		0.0093
(0.0814) 		0.685
(0.862) 		0.556
(0.775) 		0.362
(0.653) 		0.683
(0.862)
1p gain 87 (24%) 279 0.131
(0.402) 		0.123
(0.39) 		0.798
(0.93) 		0.979
(1.00) 		0.872
(0.969) 		0.352
(0.651) 		0.567
(0.779) 		0.924
(0.989) 		0.799
(0.93) 		0.496
(0.753)
6q gain 48 (13%) 318 0.308
(0.619) 		0.583
(0.789) 		0.856
(0.964) 		0.331
(0.636) 		0.943
(0.989) 		0.689
(0.863) 		0.354
(0.651) 		0.404
(0.687) 		0.834
(0.955) 		0.648
(0.838)
9p gain 16 (4%) 350 0.307
(0.618) 		0.204
(0.504) 		0.374
(0.662) 		0.835
(0.955) 		0.347
(0.65) 		0.912
(0.984) 		0.904
(0.981) 		0.61
(0.811) 		0.126
(0.396) 		0.266
(0.574)
9q gain 21 (6%) 345 0.66
(0.845) 		0.657
(0.845) 		0.133
(0.402) 		0.929
(0.989) 		0.564
(0.778) 		0.493
(0.753) 		0.885
(0.974) 		0.415
(0.698) 		0.476
(0.743) 		0.556
(0.775)
10p gain 12 (3%) 354 0.498
(0.753) 		0.93
(0.989) 		0.867
(0.968) 		0.545
(0.77) 		0.711
(0.876) 		1
(1.00) 		0.262
(0.569) 		0.558
(0.775) 		1
(1.00) 		0.905
(0.981)
10q gain 3 (1%) 363 0.378
(0.662) 		0.356
(0.651) 		0.636
(0.832) 		0.639
(0.835) 		0.778
(0.918) 		0.726
(0.892) 		0.269
(0.577) 		0.689
(0.863)
14q gain 41 (11%) 325 0.393
(0.679) 		0.399
(0.684) 		0.348
(0.651) 		0.154
(0.44) 		0.835
(0.955) 		0.915
(0.985) 		0.513
(0.758) 		0.508
(0.758) 		0.768
(0.917) 		0.967
(1.00)
1q loss 28 (8%) 338 0.0665
(0.265) 		0.0548
(0.246) 		0.969
(1.00) 		0.466
(0.739) 		0.117
(0.38) 		0.354
(0.651) 		0.368
(0.661) 		0.938
(0.989) 		0.284
(0.593) 		0.357
(0.651)
3p loss 61 (17%) 305 0.0598
(0.255) 		0.82
(0.945) 		0.495
(0.753) 		0.326
(0.636) 		0.107
(0.349) 		0.156
(0.44) 		0.0605
(0.255) 		0.66
(0.845) 		0.522
(0.759) 		0.411
(0.692)
5p loss 79 (22%) 287 0.853
(0.964) 		0.161
(0.451) 		0.881
(0.971) 		0.862
(0.967) 		0.842
(0.957) 		0.0769
(0.285) 		0.512
(0.758) 		0.257
(0.564) 		0.208
(0.508) 		0.39
(0.677)
5q loss 99 (27%) 267 0.588
(0.79) 		0.0556
(0.248) 		0.648
(0.838) 		0.36
(0.652) 		0.862
(0.967) 		0.0503
(0.237) 		0.908
(0.982) 		0.578
(0.786) 		0.421
(0.7) 		0.609
(0.81)
7p loss 18 (5%) 348 0.83
(0.953) 		0.0542
(0.246) 		0.0944
(0.327) 		0.557
(0.775) 		0.423
(0.7) 		0.842
(0.957) 		0.649
(0.838) 		0.71
(0.876) 		0.169
(0.459) 		0.752
(0.908)
15q loss 52 (14%) 314 0.182
(0.478) 		0.356
(0.651) 		0.289
(0.598) 		0.0618
(0.255) 		0.799
(0.93) 		0.267
(0.575) 		0.647
(0.838) 		0.421
(0.7) 		0.288
(0.598) 		0.461
(0.736)
16p loss 68 (19%) 298 0.205
(0.504) 		0.0949
(0.327) 		0.064
(0.261) 		0.36
(0.652) 		0.0614
(0.255) 		0.155
(0.44) 		0.235
(0.535) 		0.194
(0.493) 		0.134
(0.402) 		0.306
(0.618)
17q loss 64 (17%) 302 0.142
(0.415) 		0.133
(0.402) 		0.131
(0.402) 		0.541
(0.769) 		0.925
(0.989) 		0.495
(0.753) 		0.509
(0.758) 		0.87
(0.969) 		0.0623
(0.255) 		1
(1.00)
18q loss 100 (27%) 266 0.452
(0.727) 		0.88
(0.971) 		0.298
(0.61) 		0.49
(0.753) 		0.445
(0.722) 		0.435
(0.713) 		0.75
(0.908) 		0.23
(0.529) 		0.558
(0.775) 		0.173
(0.463)
21q loss 70 (19%) 296 0.101
(0.339) 		0.475
(0.743) 		0.469
(0.74) 		0.932
(0.989) 		0.93
(0.989) 		0.494
(0.753) 		0.337
(0.637) 		0.747
(0.908) 		0.595
(0.798) 		0.768
(0.917)
22q loss 39 (11%) 327 0.403
(0.687) 		0.421
(0.7) 		0.953
(0.994) 		0.94
(0.989) 		0.241
(0.541) 		0.963
(1.00) 		0.864
(0.967) 		0.699
(0.866) 		0.707
(0.875) 		0.773
(0.917)
'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
1Q GAIN MUTATED 77 44 50
1Q GAIN WILD-TYPE 24 95 76

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.19

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
1Q GAIN MUTATED 73 38 60
1Q GAIN WILD-TYPE 64 66 65

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.23

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
1Q GAIN MUTATED 37 44 76
1Q GAIN WILD-TYPE 55 61 63

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.093

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
2P GAIN MUTATED 24 15 28
2P GAIN WILD-TYPE 77 124 98

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.049

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
2P GAIN MUTATED 22 11 34
2P GAIN WILD-TYPE 115 93 91

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00772 (Fisher's exact test), Q value = 0.075

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
2P GAIN MUTATED 19 11 28 9
2P GAIN WILD-TYPE 88 94 68 49

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0044

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
2P GAIN MUTATED 7 23 24 11
2P GAIN WILD-TYPE 84 124 50 27

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

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.2

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
2P GAIN MUTATED 12 28 23
2P GAIN WILD-TYPE 80 77 116

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.17

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
2P GAIN MUTATED 23 31 9
2P GAIN WILD-TYPE 146 106 21

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00794 (Fisher's exact test), Q value = 0.075

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
2Q GAIN MUTATED 22 14 29
2Q GAIN WILD-TYPE 79 125 97

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.011

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
2Q GAIN MUTATED 17 12 36
2Q GAIN WILD-TYPE 120 92 89

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.093

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
2Q GAIN MUTATED 15 13 28 9
2Q GAIN WILD-TYPE 92 92 68 49

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.003

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
2Q GAIN MUTATED 6 22 24 11
2Q GAIN WILD-TYPE 85 125 50 27

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00212 (Fisher's exact test), Q value = 0.03

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
2Q GAIN MUTATED 19 33 9
2Q GAIN WILD-TYPE 150 104 21

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'RPPA_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.23

Table S15.  Gene #5: '3p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
3P GAIN MUTATED 14 5 5 7
3P GAIN WILD-TYPE 33 53 21 31

Figure S15.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.13

Table S16.  Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 58 35 49
3P GAIN MUTATED 10 5 7 9
3P GAIN WILD-TYPE 17 53 28 40

Figure S16.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'RPPA_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.12

Table S17.  Gene #6: '3q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
3Q GAIN MUTATED 18 7 6 9
3Q GAIN WILD-TYPE 29 51 20 29

Figure S17.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.23

Table S18.  Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 58 35 49
3Q GAIN MUTATED 11 8 10 11
3Q GAIN WILD-TYPE 16 50 25 38

Figure S18.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.23

Table S19.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
3Q GAIN MUTATED 18 24 30
3Q GAIN WILD-TYPE 119 80 95

Figure S19.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.026

Table S20.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
4P GAIN MUTATED 22 10 24
4P GAIN WILD-TYPE 79 129 102

Figure S20.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0458 (Fisher's exact test), Q value = 0.23

Table S21.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
4P GAIN MUTATED 13 32 6 4
4P GAIN WILD-TYPE 78 115 68 34

Figure S21.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.093

Table S22.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
4Q GAIN MUTATED 16 9 22
4Q GAIN WILD-TYPE 85 130 104

Figure S22.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.21

Table S23.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
4Q GAIN MUTATED 8 29 6 4
4Q GAIN WILD-TYPE 83 118 68 34

Figure S23.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.013

Table S24.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
5P GAIN MUTATED 21 16 39
5P GAIN WILD-TYPE 80 123 87

Figure S24.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.09

Table S25.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
5Q GAIN MUTATED 15 11 26
5Q GAIN WILD-TYPE 86 128 100

Figure S25.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.01

Table S26.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
6P GAIN MUTATED 56 43 45
6P GAIN WILD-TYPE 45 96 81

Figure S26.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0027

Table S27.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
6P GAIN MUTATED 52 40 52
6P GAIN WILD-TYPE 77 104 41

Figure S27.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.15

Table S28.  Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
6P GAIN MUTATED 49 47 26 22
6P GAIN WILD-TYPE 58 58 70 36

Figure S28.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.03

Table S29.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
6P GAIN MUTATED 21 32 28 59 0
6P GAIN WILD-TYPE 26 70 51 55 8

Figure S29.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0074

Table S30.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
6P GAIN MUTATED 27 34 73
6P GAIN WILD-TYPE 65 71 66

Figure S30.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.027

Table S31.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
6P GAIN MUTATED 83 40 11
6P GAIN WILD-TYPE 86 97 19

Figure S31.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S32.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
7P GAIN MUTATED 57 56 90
7P GAIN WILD-TYPE 44 83 36

Figure S32.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.12

Table S33.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
7P GAIN MUTATED 65 57 81
7P GAIN WILD-TYPE 72 47 44

Figure S33.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0015

Table S34.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
7Q GAIN MUTATED 54 58 88
7Q GAIN WILD-TYPE 47 81 38

Figure S34.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00593 (Fisher's exact test), Q value = 0.064

Table S35.  Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
7Q GAIN MUTATED 62 57 81
7Q GAIN WILD-TYPE 75 47 44

Figure S35.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.08

Table S36.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
7Q GAIN MUTATED 56 64 61
7Q GAIN WILD-TYPE 36 41 78

Figure S36.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S37.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
8P GAIN MUTATED 25 28 68
8P GAIN WILD-TYPE 76 111 58

Figure S37.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.1

Table S38.  Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
8P GAIN MUTATED 39 28 54
8P GAIN WILD-TYPE 98 76 71

Figure S38.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0355 (Fisher's exact test), Q value = 0.19

Table S39.  Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
8P GAIN MUTATED 40 32 38 11
8P GAIN WILD-TYPE 67 73 58 47

Figure S39.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S40.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
8Q GAIN MUTATED 41 42 86
8Q GAIN WILD-TYPE 60 97 40

Figure S40.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.02

Table S41.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
8Q GAIN MUTATED 47 65 57
8Q GAIN WILD-TYPE 82 79 36

Figure S41.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.049

Table S42.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
8Q GAIN MUTATED 59 38 72
8Q GAIN WILD-TYPE 78 66 53

Figure S42.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.064

Table S43.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
11P GAIN MUTATED 6 8 21
11P GAIN WILD-TYPE 95 131 105

Figure S43.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.022

Table S44.  Gene #21: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
11P GAIN MUTATED 8 5 22
11P GAIN WILD-TYPE 129 99 103

Figure S44.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00777 (Fisher's exact test), Q value = 0.075

Table S45.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
11P GAIN MUTATED 8 9 17 1
11P GAIN WILD-TYPE 99 96 79 57

Figure S45.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.15

Table S46.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
11P GAIN MUTATED 3 16 7 5 2
11P GAIN WILD-TYPE 44 86 72 109 6

Figure S46.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00628 (Fisher's exact test), Q value = 0.064

Table S47.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
11P GAIN MUTATED 3 16 13 1
11P GAIN WILD-TYPE 88 131 61 37

Figure S47.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.12

Table S48.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
11P GAIN MUTATED 10 20 1
11P GAIN WILD-TYPE 159 117 29

Figure S48.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

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

Table S49.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
11Q GAIN MUTATED 2 7 20
11Q GAIN WILD-TYPE 99 132 106

Figure S49.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.039

Table S50.  Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
11Q GAIN MUTATED 4 7 18
11Q GAIN WILD-TYPE 133 97 107

Figure S50.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.022

Table S51.  Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
11Q GAIN MUTATED 4 11 14 0
11Q GAIN WILD-TYPE 103 94 82 58

Figure S51.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.00598 (Fisher's exact test), Q value = 0.064

Table S52.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
11Q GAIN MUTATED 1 13 7 3 2
11Q GAIN WILD-TYPE 46 89 72 111 6

Figure S52.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.015

Table S53.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
11Q GAIN MUTATED 1 14 11 0
11Q GAIN WILD-TYPE 90 133 63 38

Figure S53.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.1

Table S54.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
11Q GAIN MUTATED 7 16 0
11Q GAIN WILD-TYPE 162 121 30

Figure S54.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.015

Table S55.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
12P GAIN MUTATED 18 13 34
12P GAIN WILD-TYPE 83 126 92

Figure S55.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.096

Table S56.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
12P GAIN MUTATED 30 9 26
12P GAIN WILD-TYPE 107 95 99

Figure S56.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.11

Table S57.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
12Q GAIN MUTATED 10 8 21
12Q GAIN WILD-TYPE 91 131 105

Figure S57.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S58.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
13Q GAIN MUTATED 31 17 46
13Q GAIN WILD-TYPE 70 122 80

Figure S58.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S59.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
13Q GAIN MUTATED 32 22 40
13Q GAIN WILD-TYPE 97 122 53

Figure S59.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

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

Table S60.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
13Q GAIN MUTATED 26 20 48
13Q GAIN WILD-TYPE 111 84 77

Figure S60.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00626 (Fisher's exact test), Q value = 0.064

Table S61.  Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
13Q GAIN MUTATED 30 29 30 5
13Q GAIN WILD-TYPE 77 76 66 53

Figure S61.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

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

Table S62.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
15Q GAIN MUTATED 15 23 47
15Q GAIN WILD-TYPE 86 116 79

Figure S62.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.047

Table S63.  Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
15Q GAIN MUTATED 20 25 40
15Q GAIN WILD-TYPE 117 79 85

Figure S63.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
15Q GAIN MUTATED 16 26 32 11
15Q GAIN WILD-TYPE 91 79 64 47

Figure S64.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.025

Table S65.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
16P GAIN MUTATED 15 12 31
16P GAIN WILD-TYPE 86 127 95

Figure S65.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.19

Table S66.  Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
16P GAIN MUTATED 17 18 23
16P GAIN WILD-TYPE 112 126 70

Figure S66.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

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

Table S67.  Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
16P GAIN MUTATED 12 13 33
16P GAIN WILD-TYPE 125 91 92

Figure S67.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0071

Table S68.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
16Q GAIN MUTATED 12 6 26
16Q GAIN WILD-TYPE 89 133 100

Figure S68.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0011

Table S69.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
16Q GAIN MUTATED 7 7 30
16Q GAIN WILD-TYPE 130 97 95

Figure S69.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.19

Table S70.  Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
16Q GAIN MUTATED 10 10 20 4
16Q GAIN WILD-TYPE 97 95 76 54

Figure S70.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.00908 (Fisher's exact test), Q value = 0.081

Table S71.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
17P GAIN MUTATED 13 6 18
17P GAIN WILD-TYPE 88 133 108

Figure S71.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.019

Table S72.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
17P GAIN MUTATED 10 8 19
17P GAIN WILD-TYPE 119 136 74

Figure S72.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.23

Table S73.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
17Q GAIN MUTATED 22 19 24
17Q GAIN WILD-TYPE 107 125 69

Figure S73.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.034

Table S74.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
18P GAIN MUTATED 18 10 27
18P GAIN WILD-TYPE 83 129 99

Figure S74.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.015

Table S75.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
18Q GAIN MUTATED 17 6 21
18Q GAIN WILD-TYPE 84 133 105

Figure S75.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 0.058

Table S76.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
19P GAIN MUTATED 16 12 29
19P GAIN WILD-TYPE 85 127 97

Figure S76.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.15

Table S77.  Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
19P GAIN MUTATED 17 17 23
19P GAIN WILD-TYPE 112 127 70

Figure S77.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.022

Table S78.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
19P GAIN MUTATED 20 7 30
19P GAIN WILD-TYPE 117 97 95

Figure S78.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.09

Table S79.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
19Q GAIN MUTATED 17 12 27
19Q GAIN WILD-TYPE 84 127 99

Figure S79.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.12

Table S80.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
19Q GAIN MUTATED 15 18 23
19Q GAIN WILD-TYPE 114 126 70

Figure S80.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0044

Table S81.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
19Q GAIN MUTATED 18 6 32
19Q GAIN WILD-TYPE 119 98 93

Figure S81.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S82.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
20P GAIN MUTATED 48 29 70
20P GAIN WILD-TYPE 53 110 56

Figure S82.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.009 (Fisher's exact test), Q value = 0.081

Table S83.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
20P GAIN MUTATED 47 50 50
20P GAIN WILD-TYPE 82 94 43

Figure S83.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0049

Table S84.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
20P GAIN MUTATED 44 34 69
20P GAIN WILD-TYPE 93 70 56

Figure S84.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.13

Table S85.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
20P GAIN MUTATED 38 40 51 18
20P GAIN WILD-TYPE 69 65 45 40

Figure S85.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S86.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
20Q GAIN MUTATED 64 37 78
20Q GAIN WILD-TYPE 37 102 48

Figure S86.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.11

Table S87.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
20Q GAIN MUTATED 61 61 57
20Q GAIN WILD-TYPE 68 83 36

Figure S87.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.048

Table S88.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
20Q GAIN MUTATED 61 42 76
20Q GAIN WILD-TYPE 76 62 49

Figure S88.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.23

Table S89.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
21Q GAIN MUTATED 24 19 24
21Q GAIN WILD-TYPE 105 125 69

Figure S89.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0092

Table S90.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
22Q GAIN MUTATED 46 31 49
22Q GAIN WILD-TYPE 55 108 77

Figure S90.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0044

Table S91.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
XP GAIN MUTATED 21 5 15
XP GAIN WILD-TYPE 80 134 111

Figure S91.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.025

Table S92.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
XP GAIN MUTATED 16 7 18
XP GAIN WILD-TYPE 113 137 75

Figure S92.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00728 (Fisher's exact test), Q value = 0.073

Table S93.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
XP GAIN MUTATED 14 5 22
XP GAIN WILD-TYPE 123 99 103

Figure S93.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.02

Table S94.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
XP GAIN MUTATED 2 13 23
XP GAIN WILD-TYPE 90 92 116

Figure S94.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0033

Table S95.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
XQ GAIN MUTATED 22 5 16
XQ GAIN WILD-TYPE 79 134 110

Figure S95.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0079

Table S96.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
XQ GAIN MUTATED 18 6 19
XQ GAIN WILD-TYPE 111 138 74

Figure S96.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00446 (Fisher's exact test), Q value = 0.052

Table S97.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
XQ GAIN MUTATED 18 4 21
XQ GAIN WILD-TYPE 119 100 104

Figure S97.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0067

Table S98.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
XQ GAIN MUTATED 1 13 23
XQ GAIN WILD-TYPE 91 92 116

Figure S98.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.23

Table S99.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
1P LOSS MUTATED 15 13 25
1P LOSS WILD-TYPE 86 126 101

Figure S99.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0071

Table S100.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
1P LOSS MUTATED 13 14 26
1P LOSS WILD-TYPE 116 130 67

Figure S100.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.09

Table S101.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
1P LOSS MUTATED 18 8 27
1P LOSS WILD-TYPE 119 96 98

Figure S101.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00933 (Fisher's exact test), Q value = 0.081

Table S102.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
1P LOSS MUTATED 8 23 4 15 2
1P LOSS WILD-TYPE 39 79 75 99 6

Figure S102.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.23

Table S103.  Gene #44: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
2P LOSS MUTATED 4 15 3 3
2P LOSS WILD-TYPE 43 43 23 35

Figure S103.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.11

Table S104.  Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 58 35 49
2P LOSS MUTATED 1 7 3 14
2P LOSS WILD-TYPE 26 51 32 35

Figure S104.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.19

Table S105.  Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
2P LOSS MUTATED 16 21 6 8
2P LOSS WILD-TYPE 91 84 90 50

Figure S105.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.039

Table S106.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
2P LOSS MUTATED 7 7 7 28 1
2P LOSS WILD-TYPE 40 95 72 86 7

Figure S106.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.091

Table S107.  Gene #45: '2q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
2Q LOSS MUTATED 4 16 4 2
2Q LOSS WILD-TYPE 43 42 22 36

Figure S107.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0017 (Fisher's exact test), Q value = 0.026

Table S108.  Gene #45: '2q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 58 35 49
2Q LOSS MUTATED 1 6 3 16
2Q LOSS WILD-TYPE 26 52 32 33

Figure S108.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00793 (Fisher's exact test), Q value = 0.075

Table S109.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
2Q LOSS MUTATED 7 8 8 28 1
2Q LOSS WILD-TYPE 40 94 71 86 7

Figure S109.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.23

Table S110.  Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
3Q LOSS MUTATED 13 14 26
3Q LOSS WILD-TYPE 88 125 100

Figure S110.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.1

Table S111.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
4P LOSS MUTATED 23 20 23 9
4P LOSS WILD-TYPE 68 127 51 29

Figure S111.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.19

Table S112.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
4Q LOSS MUTATED 21 19 33 12
4Q LOSS WILD-TYPE 86 86 63 46

Figure S112.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00559 (Fisher's exact test), Q value = 0.062

Table S113.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
4Q LOSS MUTATED 23 21 25 11
4Q LOSS WILD-TYPE 68 126 49 27

Figure S113.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.058

Table S114.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
6P LOSS MUTATED 15 18 35
6P LOSS WILD-TYPE 86 121 91

Figure S114.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.098

Table S115.  Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
6P LOSS MUTATED 25 11 32
6P LOSS WILD-TYPE 112 93 93

Figure S115.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.19

Table S116.  Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
6P LOSS MUTATED 23 14 25 6
6P LOSS WILD-TYPE 84 91 71 52

Figure S116.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.21

Table S117.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
6P LOSS MUTATED 9 26 13 13 3
6P LOSS WILD-TYPE 38 76 66 101 5

Figure S117.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.16

Table S118.  Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
6P LOSS MUTATED 16 27 17
6P LOSS WILD-TYPE 76 78 122

Figure S118.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.16

Table S119.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
6P LOSS MUTATED 21 32 7
6P LOSS WILD-TYPE 148 105 23

Figure S119.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S120.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
6Q LOSS MUTATED 61 38 73
6Q LOSS WILD-TYPE 40 101 53

Figure S120.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.11

Table S121.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
6Q LOSS MUTATED 72 55 45
6Q LOSS WILD-TYPE 57 89 48

Figure S121.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

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

Table S122.  Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
6Q LOSS MUTATED 72 34 66
6Q LOSS WILD-TYPE 65 70 59

Figure S122.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.09

Table S123.  Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
7Q LOSS MUTATED 3 4 10
7Q LOSS WILD-TYPE 126 140 83

Figure S123.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.17

Table S124.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
8P LOSS MUTATED 26 27 9 4
8P LOSS WILD-TYPE 65 120 65 34

Figure S124.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.00795 (Fisher's exact test), Q value = 0.075

Table S125.  Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
8Q LOSS MUTATED 16 4 7
8Q LOSS WILD-TYPE 113 140 86

Figure S125.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.11

Table S126.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
8Q LOSS MUTATED 3 5 18
8Q LOSS WILD-TYPE 89 100 121

Figure S126.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0044

Table S127.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
9P LOSS MUTATED 60 77 99
9P LOSS WILD-TYPE 41 62 27

Figure S127.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.036

Table S128.  Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
9P LOSS MUTATED 86 56 94
9P LOSS WILD-TYPE 51 48 31

Figure S128.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.096

Table S129.  Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
9Q LOSS MUTATED 57 53 75
9Q LOSS WILD-TYPE 80 51 50

Figure S129.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.21

Table S130.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
9Q LOSS MUTATED 26 53 30 60 7
9Q LOSS WILD-TYPE 21 49 49 54 1

Figure S130.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S131.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
10P LOSS MUTATED 55 51 98
10P LOSS WILD-TYPE 46 88 28

Figure S131.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.02

Table S132.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
10P LOSS MUTATED 69 49 86
10P LOSS WILD-TYPE 68 55 39

Figure S132.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.11

Table S133.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
10P LOSS MUTATED 59 52 66 27
10P LOSS WILD-TYPE 48 53 30 31

Figure S133.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S134.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
10Q LOSS MUTATED 51 63 110
10Q LOSS WILD-TYPE 50 76 16

Figure S134.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.006

Table S135.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
10Q LOSS MUTATED 74 55 95
10Q LOSS WILD-TYPE 63 49 30

Figure S135.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00239 (Fisher's exact test), Q value = 0.033

Table S136.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
10Q LOSS MUTATED 60 58 74 32
10Q LOSS WILD-TYPE 47 47 22 26

Figure S136.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.13

Table S137.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
10Q LOSS MUTATED 26 66 40 75 8
10Q LOSS WILD-TYPE 21 36 39 39 0

Figure S137.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.12

Table S138.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
11P LOSS MUTATED 43 36 47
11P LOSS WILD-TYPE 58 103 79

Figure S138.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.1

Table S139.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
11Q LOSS MUTATED 52 45 51
11Q LOSS WILD-TYPE 49 94 75

Figure S139.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.029

Table S140.  Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
11Q LOSS MUTATED 47 34 32 35
11Q LOSS WILD-TYPE 60 71 64 23

Figure S140.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.11

Table S141.  Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
12P LOSS MUTATED 13 18 28
12P LOSS WILD-TYPE 124 86 97

Figure S141.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.19

Table S142.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
12Q LOSS MUTATED 19 17 31
12Q LOSS WILD-TYPE 82 122 95

Figure S142.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.00806 (Fisher's exact test), Q value = 0.075

Table S143.  Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
12Q LOSS MUTATED 33 16 18
12Q LOSS WILD-TYPE 96 128 75

Figure S143.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.091

Table S144.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
13Q LOSS MUTATED 26 42 12
13Q LOSS WILD-TYPE 103 102 81

Figure S144.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.19

Table S145.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
13Q LOSS MUTATED 19 17 24 20
13Q LOSS WILD-TYPE 88 88 72 38

Figure S145.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S146.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
14Q LOSS MUTATED 26 27 59
14Q LOSS WILD-TYPE 75 112 67

Figure S146.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.00907 (Fisher's exact test), Q value = 0.081

Table S147.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
14Q LOSS MUTATED 30 33 49
14Q LOSS WILD-TYPE 107 71 76

Figure S147.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0331 (Fisher's exact test), Q value = 0.19

Table S148.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
14Q LOSS MUTATED 32 32 38 10
14Q LOSS WILD-TYPE 75 73 58 48

Figure S148.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00571 (Fisher's exact test), Q value = 0.062

Table S149.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
14Q LOSS MUTATED 14 33 23 26 7
14Q LOSS WILD-TYPE 33 69 56 88 1

Figure S149.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.11

Table S150.  Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
16Q LOSS MUTATED 11 23 3 16
16Q LOSS WILD-TYPE 36 35 23 22

Figure S150.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.2

Table S151.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
16Q LOSS MUTATED 50 28 28
16Q LOSS WILD-TYPE 87 76 97

Figure S151.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.19

Table S152.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
16Q LOSS MUTATED 36 30 18 22
16Q LOSS WILD-TYPE 71 75 78 36

Figure S152.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.062

Table S153.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
17P LOSS MUTATED 53 54 20
17P LOSS WILD-TYPE 76 90 73

Figure S153.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

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

Table S154.  Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
18P LOSS MUTATED 30 28 46
18P LOSS WILD-TYPE 107 76 79

Figure S154.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.16

Table S155.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
18P LOSS MUTATED 9 29 19 36 6
18P LOSS WILD-TYPE 38 73 60 78 2

Figure S155.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.19

Table S156.  Gene #75: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 58 35 49
19P LOSS MUTATED 4 9 4 17
19P LOSS WILD-TYPE 23 49 31 32

Figure S156.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.15

Table S157.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
19Q LOSS MUTATED 29 20 24
19Q LOSS WILD-TYPE 72 119 102

Figure S157.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.23

Table S158.  Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
19Q LOSS MUTATED 33 20 20
19Q LOSS WILD-TYPE 96 124 73

Figure S158.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.14

Table S159.  Gene #77: '20p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
20P LOSS MUTATED 14 7 2 3
20P LOSS WILD-TYPE 93 98 94 55

Figure S159.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.11

Table S160.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
20P LOSS MUTATED 12 6 5 0
20P LOSS WILD-TYPE 79 141 69 38

Figure S160.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0093 (Fisher's exact test), Q value = 0.081

Table S161.  Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
20Q LOSS MUTATED 7 2 0 0
20Q LOSS WILD-TYPE 100 103 96 58

Figure S161.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.18

Table S162.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
XP LOSS MUTATED 24 29 44
XP LOSS WILD-TYPE 77 110 82

Figure S162.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S163.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
XP LOSS MUTATED 50 18 29
XP LOSS WILD-TYPE 79 126 64

Figure S163.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.02

Table S164.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
XP LOSS MUTATED 44 14 39
XP LOSS WILD-TYPE 93 90 86

Figure S164.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00396 (Fisher's exact test), Q value = 0.048

Table S165.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
XP LOSS MUTATED 38 16 30 13
XP LOSS WILD-TYPE 69 89 66 45

Figure S165.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.15

Table S166.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
XP LOSS MUTATED 9 21 18 41 4
XP LOSS WILD-TYPE 38 81 61 73 4

Figure S166.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.18

Table S167.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
XP LOSS MUTATED 20 21 47
XP LOSS WILD-TYPE 72 84 92

Figure S167.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.21

Table S168.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
XQ LOSS MUTATED 23 28 42
XQ LOSS WILD-TYPE 78 111 84

Figure S168.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S169.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
XQ LOSS MUTATED 48 18 27
XQ LOSS WILD-TYPE 81 126 66

Figure S169.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.015

Table S170.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
XQ LOSS MUTATED 40 13 40
XQ LOSS WILD-TYPE 97 91 85

Figure S170.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00625 (Fisher's exact test), Q value = 0.064

Table S171.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
XQ LOSS MUTATED 34 15 31 13
XQ LOSS WILD-TYPE 73 90 65 45

Figure S171.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.19

Table S172.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
XQ LOSS MUTATED 21 20 46
XQ LOSS WILD-TYPE 71 85 93

Figure S172.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/15098586/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/15111349/SKCM-TM.transferedmergedcluster.txt

  • Number of patients = 366

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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