Correlation between copy number variation genes (focal events) and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 54 focal events and 10 molecular subtypes across 367 patients, 163 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p12 cnv correlated to 'MRNASEQ_CNMF'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_1q44 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_4q12 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • amp_5q35.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_6p24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6q12 cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • amp_7p22.1 cnv correlated to 'CN_CNMF'.

  • amp_7q34 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_11q13.3 cnv correlated to 'CN_CNMF'.

  • amp_12q14.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q31.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_15q26.2 cnv correlated to 'CN_CNMF'.

  • amp_17q25.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20q13.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_22q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_1p22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_2q37.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3p25.1 cnv correlated to 'CN_CNMF'.

  • del_3q13.31 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

  • del_4p16.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5p15.31 cnv correlated to 'CN_CNMF'.

  • del_5q12.1 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • del_5q31.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • del_6q21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_6q26 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_8p23.3 cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10q21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10q23.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10q26.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_11p15.5 cnv correlated to 'CN_CNMF'.

  • del_11q23.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_12q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_14q23.3 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q32.31 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_15q13.3 cnv correlated to 'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_15q21.1 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • del_16p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • del_16q12.1 cnv correlated to 'CN_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_16q24.3 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_17p13.3 cnv correlated to 'RPPA_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_xp21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 54 focal 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, 163 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
amp 6p24 3 211 (57%) 156 1e-05
(0.000245) 		1e-05
(0.000245) 		0.0268
(0.114) 		0.05
(0.165) 		0.00677
(0.043) 		0.00421
(0.0316) 		0.00414
(0.0316) 		9e-05
(0.00157) 		0.0002
(0.00292) 		0.00014
(0.00236)
del xp21 1 86 (23%) 281 0.0301
(0.12) 		2e-05
(0.000432) 		0.141
(0.308) 		0.249
(0.418) 		0.00931
(0.0559) 		0.0042
(0.0316) 		0.00237
(0.0213) 		0.0198
(0.095) 		0.0437
(0.154) 		0.00073
(0.00876)
amp 1q44 201 (55%) 166 2e-05
(0.000432) 		0.0661
(0.195) 		0.00067
(0.00822) 		0.0846
(0.225) 		0.00149
(0.0161) 		0.072
(0.202) 		0.00017
(0.00255) 		0.0016
(0.0169) 		0.00509
(0.0357) 		0.0126
(0.0678)
del 2q37 3 93 (25%) 274 0.0163
(0.0823) 		0.0106
(0.0607) 		0.174
(0.346) 		0.0233
(0.107) 		0.0441
(0.154) 		0.0018
(0.0183) 		0.0124
(0.0678) 		0.0343
(0.13) 		0.241
(0.409) 		0.647
(0.74)
del 9p21 3 278 (76%) 89 1e-05
(0.000245) 		0.00061
(0.00766) 		0.00821
(0.051) 		0.206
(0.375) 		0.00253
(0.0224) 		0.00333
(0.0272) 		0.0298
(0.12) 		0.503
(0.636) 		0.126
(0.286) 		0.00262
(0.0224)
amp 1q21 3 203 (55%) 164 1e-05
(0.000245) 		0.13
(0.293) 		0.00117
(0.0132) 		0.0979
(0.244) 		0.00049
(0.00645) 		0.357
(0.517) 		0.0274
(0.115) 		0.0127
(0.0678) 		0.0389
(0.145) 		0.0536
(0.169)
amp 13q31 3 104 (28%) 263 1e-05
(0.000245) 		2e-05
(0.000432) 		0.214
(0.382) 		0.18
(0.352) 		6e-05
(0.0012) 		0.0105
(0.0607) 		0.704
(0.784) 		0.584
(0.698) 		0.127
(0.286) 		0.0128
(0.0678)
del 1p22 1 97 (26%) 270 0.00017
(0.00255) 		0.00404
(0.0316) 		0.303
(0.458) 		0.0545
(0.169) 		0.0175
(0.0866) 		0.00672
(0.043) 		0.113
(0.27) 		0.646
(0.74) 		0.042
(0.152) 		0.694
(0.779)
del 4q34 3 110 (30%) 257 0.00685
(0.043) 		0.371
(0.527) 		0.748
(0.817) 		0.722
(0.801) 		0.0314
(0.123) 		0.00476
(0.0338) 		0.589
(0.698) 		0.00313
(0.026) 		0.17
(0.343) 		0.0489
(0.164)
del 9p23 249 (68%) 118 0.00017
(0.00255) 		0.0314
(0.123) 		0.0422
(0.152) 		0.252
(0.418) 		0.0443
(0.154) 		0.16
(0.331) 		0.0916
(0.238) 		0.0893
(0.235) 		0.704
(0.784) 		0.00127
(0.014)
amp 20q13 33 188 (51%) 179 1e-05
(0.000245) 		0.0191
(0.093) 		0.017
(0.085) 		0.0984
(0.244) 		0.118
(0.275) 		0.0437
(0.154) 		0.251
(0.418) 		0.695
(0.779) 		0.748
(0.817) 		0.264
(0.429)
del 1p36 31 81 (22%) 286 0.00573
(0.0397) 		0.00637
(0.0418) 		0.071
(0.201) 		0.801
(0.854) 		0.107
(0.259) 		0.0246
(0.109) 		0.0115
(0.0643) 		0.147
(0.317) 		0.169
(0.342) 		0.29
(0.447)
del 10p15 3 199 (54%) 168 1e-05
(0.000245) 		0.00462
(0.0333) 		0.739
(0.813) 		0.585
(0.698) 		0.00457
(0.0333) 		0.00102
(0.0117) 		0.9
(0.926) 		0.195
(0.364) 		0.3
(0.457) 		0.111
(0.267)
del 10q23 31 230 (63%) 137 1e-05
(0.000245) 		0.00227
(0.0208) 		0.863
(0.896) 		0.681
(0.769) 		0.0342
(0.13) 		0.0199
(0.095) 		0.693
(0.779) 		0.261
(0.426) 		0.302
(0.458) 		0.372
(0.527)
del 10q26 3 236 (64%) 131 1e-05
(0.000245) 		0.00366
(0.0295) 		0.982
(0.987) 		1
(1.00) 		0.00642
(0.0418) 		0.00627
(0.0418) 		0.67
(0.759) 		0.19
(0.361) 		0.117
(0.275) 		0.225
(0.393)
del 14q23 3 120 (33%) 247 9e-05
(0.00157) 		0.253
(0.418) 		0.72
(0.8) 		0.0138
(0.0717) 		0.00602
(0.0411) 		0.0302
(0.12) 		0.0548
(0.169) 		0.555
(0.685) 		0.189
(0.361) 		0.331
(0.489)
del 14q32 31 117 (32%) 250 8e-05
(0.00154) 		0.0654
(0.194) 		0.607
(0.712) 		0.0294
(0.12) 		0.0115
(0.0643) 		0.0216
(0.102) 		0.19
(0.361) 		0.606
(0.712) 		0.41
(0.558) 		0.238
(0.406)
del 16q24 3 133 (36%) 234 1e-05
(0.000245) 		0.096
(0.241) 		0.0419
(0.152) 		0.513
(0.645) 		0.0254
(0.11) 		0.0246
(0.109) 		0.246
(0.414) 		0.103
(0.252) 		0.069
(0.2) 		0.189
(0.361)
amp 8q24 21 192 (52%) 175 1e-05
(0.000245) 		9e-05
(0.00157) 		0.515
(0.645) 		0.917
(0.939) 		5e-05
(0.00104) 		0.0541
(0.169) 		0.93
(0.944) 		0.125
(0.284) 		0.371
(0.527) 		0.275
(0.438)
amp 22q13 2 152 (41%) 215 0.00217
(0.0202) 		0.0442
(0.154) 		0.222
(0.39) 		0.273
(0.436) 		0.277
(0.439) 		0.535
(0.665) 		0.419
(0.565) 		0.0915
(0.238) 		0.579
(0.698) 		0.0108
(0.0614)
del 5q31 3 131 (36%) 236 1e-05
(0.000245) 		0.03
(0.12) 		0.026
(0.111) 		0.651
(0.743) 		0.244
(0.411) 		0.37
(0.527) 		0.845
(0.889) 		0.609
(0.712) 		0.589
(0.698) 		0.788
(0.851)
del 6q21 214 (58%) 153 1e-05
(0.000245) 		0.0017
(0.0177) 		0.643
(0.739) 		0.432
(0.572) 		0.00192
(0.0185) 		0.132
(0.295) 		0.501
(0.636) 		0.155
(0.326) 		0.0993
(0.245) 		0.41
(0.558)
del 6q26 221 (60%) 146 1e-05
(0.000245) 		0.00417
(0.0316) 		0.204
(0.374) 		0.204
(0.374) 		0.00634
(0.0418) 		0.0509
(0.165) 		0.399
(0.549) 		0.189
(0.361) 		0.315
(0.471) 		0.278
(0.439)
del 8p23 3 89 (24%) 278 0.00028
(0.00398) 		0.0821
(0.223) 		0.0323
(0.126) 		0.0217
(0.102) 		0.0708
(0.201) 		0.951
(0.96) 		0.29
(0.447) 		0.433
(0.572) 		0.266
(0.43) 		0.802
(0.854)
del 10q21 1 217 (59%) 150 1e-05
(0.000245) 		0.0142
(0.0724) 		0.885
(0.912) 		0.913
(0.937) 		0.0937
(0.239) 		0.0346
(0.13) 		0.502
(0.636) 		0.136
(0.302) 		0.15
(0.32) 		0.653
(0.744)
del 15q13 3 84 (23%) 283 0.0846
(0.225) 		0.0527
(0.168) 		0.0224
(0.103) 		0.203
(0.374) 		0.29
(0.447) 		0.0423
(0.152) 		0.921
(0.942) 		0.827
(0.876) 		0.00832
(0.0511) 		0.591
(0.698)
del 16p13 3 62 (17%) 305 0.00966
(0.0573) 		0.00909
(0.0552) 		0.192
(0.362) 		0.0478
(0.162) 		0.256
(0.422) 		0.567
(0.688) 		0.175
(0.347) 		0.366
(0.525) 		0.0506
(0.165) 		0.418
(0.565)
del 16q23 1 120 (33%) 247 1e-05
(0.000245) 		0.0412
(0.152) 		0.0528
(0.168) 		0.27
(0.434) 		0.0178
(0.0874) 		0.0679
(0.198) 		0.273
(0.436) 		0.0816
(0.223) 		0.136
(0.302) 		0.0928
(0.238)
amp 4q12 65 (18%) 302 0.124
(0.284) 		0.407
(0.558) 		0.209
(0.376) 		0.385
(0.537) 		0.489
(0.626) 		0.0724
(0.202) 		0.00456
(0.0333) 		0.00091
(0.0107) 		0.0617
(0.187) 		0.306
(0.461)
amp 5p15 33 110 (30%) 257 1e-05
(0.000245) 		0.284
(0.445) 		0.405
(0.556) 		0.352
(0.515) 		0.149
(0.32) 		0.191
(0.362) 		0.00184
(0.0184) 		0.179
(0.352) 		0.0827
(0.223) 		0.22
(0.388)
amp 5q35 3 59 (16%) 308 1e-05
(0.000245) 		0.0302
(0.12) 		0.46
(0.602) 		0.0512
(0.166) 		0.181
(0.353) 		0.0926
(0.238) 		0.394
(0.546) 		0.149
(0.32) 		0.053
(0.168) 		0.583
(0.698)
amp 6q12 81 (22%) 286 0.386
(0.537) 		0.463
(0.603) 		0.613
(0.712) 		0.0121
(0.0665) 		0.258
(0.423) 		0.242
(0.409) 		0.613
(0.712) 		0.0252
(0.11) 		0.234
(0.404) 		0.361
(0.521)
amp 7q34 225 (61%) 142 0.00192
(0.0185) 		0.859
(0.894) 		0.252
(0.418) 		0.557
(0.685) 		0.194
(0.364) 		0.153
(0.322) 		0.626
(0.724) 		0.203
(0.374) 		0.478
(0.616) 		0.00201
(0.019)
amp 12q14 1 58 (16%) 309 0.0221
(0.103) 		0.42
(0.565) 		0.881
(0.912) 		0.183
(0.355) 		0.276
(0.438) 		0.301
(0.457) 		0.843
(0.889) 		0.235
(0.404) 		0.318
(0.474) 		0.0251
(0.11)
amp 17q25 3 122 (33%) 245 0.00059
(0.00759) 		0.076
(0.21) 		0.197
(0.366) 		0.342
(0.503) 		0.802
(0.854) 		0.0346
(0.13) 		0.315
(0.471) 		0.0714
(0.201) 		0.484
(0.622) 		0.064
(0.191)
del 3q13 31 62 (17%) 305 0.12
(0.278) 		0.0568
(0.174) 		0.174
(0.346) 		0.063
(0.19) 		0.0245
(0.109) 		0.286
(0.445) 		0.0495
(0.165) 		0.0607
(0.185) 		0.165
(0.336) 		0.59
(0.698)
del 5q12 1 97 (26%) 270 1e-05
(0.000245) 		0.165
(0.336) 		0.00265
(0.0224) 		0.163
(0.336) 		0.339
(0.501) 		0.108
(0.259) 		0.846
(0.889) 		0.59
(0.698) 		0.608
(0.712) 		0.944
(0.955)
del 11q23 3 204 (56%) 163 1e-05
(0.000245) 		0.563
(0.687) 		0.383
(0.537) 		0.161
(0.333) 		0.169
(0.342) 		0.206
(0.375) 		0.285
(0.445) 		0.0709
(0.201) 		0.0487
(0.164) 		0.12
(0.278)
del 12q23 3 92 (25%) 275 0.0275
(0.115) 		0.01
(0.059) 		0.261
(0.426) 		0.146
(0.316) 		0.505
(0.637) 		0.732
(0.807) 		0.588
(0.698) 		0.107
(0.259) 		0.662
(0.752) 		0.376
(0.53)
del 15q21 1 91 (25%) 276 0.0478
(0.162) 		0.236
(0.404) 		0.0839
(0.225) 		0.0242
(0.109) 		0.428
(0.57) 		0.113
(0.27) 		0.877
(0.909) 		0.397
(0.548) 		0.0906
(0.238) 		0.853
(0.894)
del 19p13 3 104 (28%) 263 0.014
(0.072) 		0.292
(0.448) 		0.15
(0.32) 		0.222
(0.39) 		0.00015
(0.00245) 		0.138
(0.304) 		0.363
(0.523) 		0.0958
(0.241) 		0.546
(0.674) 		0.233
(0.404)
amp 1p12 121 (33%) 246 0.135
(0.301) 		0.963
(0.971) 		0.252
(0.418) 		0.93
(0.944) 		0.0297
(0.12) 		0.64
(0.739) 		0.506
(0.637) 		0.564
(0.687) 		0.642
(0.739) 		0.701
(0.784)
amp 7p22 1 209 (57%) 158 0.0004
(0.00553) 		0.158
(0.331) 		0.485
(0.622) 		0.3
(0.457) 		0.234
(0.404) 		0.115
(0.273) 		0.926
(0.944) 		0.426
(0.569) 		0.859
(0.894) 		0.241
(0.409)
amp 11q13 3 69 (19%) 298 0.0136
(0.0714) 		0.0729
(0.202) 		0.787
(0.851) 		0.449
(0.59) 		0.53
(0.661) 		0.795
(0.854) 		0.573
(0.694) 		0.0699
(0.201) 		0.726
(0.804) 		0.329
(0.488)
amp 15q26 2 120 (33%) 247 0.00265
(0.0224) 		0.173
(0.346) 		0.81
(0.861) 		0.492
(0.629) 		0.439
(0.579) 		0.116
(0.273) 		0.28
(0.44) 		0.564
(0.687) 		0.172
(0.345) 		0.366
(0.525)
del 3p25 1 71 (19%) 296 0.0475
(0.162) 		0.423
(0.567) 		0.465
(0.603) 		0.312
(0.469) 		0.695
(0.779) 		0.812
(0.861) 		0.159
(0.331) 		0.27
(0.434) 		0.218
(0.386) 		0.619
(0.717)
del 4p16 3 91 (25%) 276 0.562
(0.687) 		0.0706
(0.201) 		0.388
(0.538) 		0.74
(0.813) 		0.516
(0.645) 		0.0457
(0.158) 		0.988
(0.991) 		0.21
(0.376) 		0.532
(0.662) 		0.942
(0.954)
del 5p15 31 79 (22%) 288 1e-05
(0.000245) 		0.592
(0.698) 		0.0945
(0.24) 		0.796
(0.854) 		0.439
(0.579) 		0.28
(0.44) 		0.991
(0.993) 		0.43
(0.572) 		0.19
(0.361) 		0.669
(0.759)
del 11p15 5 114 (31%) 253 0.00041
(0.00553) 		0.193
(0.363) 		0.767
(0.833) 		0.855
(0.894) 		0.885
(0.912) 		0.353
(0.515) 		0.455
(0.596) 		0.0827
(0.223) 		0.208
(0.375) 		0.408
(0.558)
del 16q12 1 117 (32%) 250 1e-05
(0.000245) 		0.0665
(0.195) 		0.0923
(0.238) 		0.538
(0.666) 		0.0507
(0.165) 		0.197
(0.366) 		0.16
(0.331) 		0.0545
(0.169) 		0.35
(0.514) 		0.124
(0.284)
del 17p13 3 134 (37%) 233 0.749
(0.817) 		0.262
(0.426) 		0.0892
(0.235) 		0.0329
(0.127) 		0.216
(0.384) 		0.386
(0.537) 		0.847
(0.889) 		0.355
(0.516) 		0.354
(0.515) 		0.226
(0.393)
amp 3p13 103 (28%) 264 0.151
(0.32) 		0.799
(0.854) 		0.289
(0.447) 		0.76
(0.828) 		0.731
(0.807) 		0.42
(0.565) 		0.93
(0.944) 		0.107
(0.259) 		0.797
(0.854) 		0.859
(0.894)
amp 12q15 59 (16%) 308 0.208
(0.375) 		0.494
(0.629) 		0.12
(0.278) 		0.137
(0.302) 		0.214
(0.382) 		0.0638
(0.191) 		0.469
(0.608) 		0.32
(0.477) 		0.565
(0.687) 		0.0984
(0.244)
del 13q34 85 (23%) 282 0.782
(0.848) 		0.464
(0.603) 		0.612
(0.712) 		0.471
(0.608) 		0.177
(0.348) 		0.419
(0.565) 		0.586
(0.698) 		0.374
(0.529) 		0.38
(0.534) 		0.145
(0.316)
'amp_1p12' versus 'MRNASEQ_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #1: 'amp_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
AMP PEAK 1(1P12) MUTATED 46 18 40 17
AMP PEAK 1(1P12) WILD-TYPE 70 55 65 56

Figure S1.  Get High-res Image Gene #1: 'amp_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S2.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 2(1Q21.3) MUTATED 98 71 34
AMP PEAK 2(1Q21.3) WILD-TYPE 56 39 69

Figure S2.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.013

Table S3.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
AMP PEAK 2(1Q21.3) MUTATED 13 43 19 44 25
AMP PEAK 2(1Q21.3) WILD-TYPE 26 35 24 25 7

Figure S3.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0065

Table S4.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
AMP PEAK 2(1Q21.3) MUTATED 72 26 56 49
AMP PEAK 2(1Q21.3) WILD-TYPE 44 47 49 24

Figure S4.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.12

Table S5.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
AMP PEAK 2(1Q21.3) MUTATED 44 62 50 37
AMP PEAK 2(1Q21.3) WILD-TYPE 53 41 47 17

Figure S5.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.068

Table S6.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
AMP PEAK 2(1Q21.3) MUTATED 80 39 48 26
AMP PEAK 2(1Q21.3) WILD-TYPE 52 54 40 12

Figure S6.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.14

Table S7.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
AMP PEAK 2(1Q21.3) MUTATED 38 65 83
AMP PEAK 2(1Q21.3) WILD-TYPE 47 54 50

Figure S7.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S8.  Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 3(1Q44) MUTATED 96 70 35
AMP PEAK 3(1Q44) WILD-TYPE 58 40 68

Figure S8.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q44' versus 'RPPA_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0082

Table S9.  Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
AMP PEAK 3(1Q44) MUTATED 14 40 21 41 27
AMP PEAK 3(1Q44) WILD-TYPE 25 38 22 28 5

Figure S9.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.016

Table S10.  Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
AMP PEAK 3(1Q44) MUTATED 71 28 53 49
AMP PEAK 3(1Q44) WILD-TYPE 45 45 52 24

Figure S10.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0025

Table S11.  Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
AMP PEAK 3(1Q44) MUTATED 40 63 48 41
AMP PEAK 3(1Q44) WILD-TYPE 57 40 49 13

Figure S11.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.017

Table S12.  Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
AMP PEAK 3(1Q44) MUTATED 77 38 48 29
AMP PEAK 3(1Q44) WILD-TYPE 55 55 40 9

Figure S12.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 0.036

Table S13.  Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
AMP PEAK 3(1Q44) MUTATED 36 64 86
AMP PEAK 3(1Q44) WILD-TYPE 49 55 47

Figure S13.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.068

Table S14.  Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
AMP PEAK 3(1Q44) MUTATED 16 11 23 40 21 6 38 24 7
AMP PEAK 3(1Q44) WILD-TYPE 20 13 28 23 17 11 26 5 8

Figure S14.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.00456 (Fisher's exact test), Q value = 0.033

Table S15.  Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
AMP PEAK 5(4Q12) MUTATED 12 29 11 13
AMP PEAK 5(4Q12) WILD-TYPE 85 74 86 41

Figure S15.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.011

Table S16.  Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
AMP PEAK 5(4Q12) MUTATED 38 8 14 5
AMP PEAK 5(4Q12) WILD-TYPE 94 85 74 33

Figure S16.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S17.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 6(5P15.33) MUTATED 72 23 15
AMP PEAK 6(5P15.33) WILD-TYPE 82 87 88

Figure S17.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.018

Table S18.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
AMP PEAK 6(5P15.33) MUTATED 30 38 15 21
AMP PEAK 6(5P15.33) WILD-TYPE 67 65 82 33

Figure S18.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S19.  Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 7(5Q35.3) MUTATED 46 8 5
AMP PEAK 7(5Q35.3) WILD-TYPE 108 102 98

Figure S19.  Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.12

Table S20.  Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
AMP PEAK 7(5Q35.3) MUTATED 24 11 8 16
AMP PEAK 7(5Q35.3) WILD-TYPE 87 111 26 83

Figure S20.  Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S21.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 8(6P24.3) MUTATED 105 71 35
AMP PEAK 8(6P24.3) WILD-TYPE 49 39 68

Figure S21.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S22.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
AMP PEAK 8(6P24.3) MUTATED 71 48 21 70
AMP PEAK 8(6P24.3) WILD-TYPE 40 74 13 29

Figure S22.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'RPPA_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.11

Table S23.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
AMP PEAK 8(6P24.3) MUTATED 17 45 22 50 16
AMP PEAK 8(6P24.3) WILD-TYPE 22 33 21 19 16

Figure S23.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.17

Table S24.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
AMP PEAK 8(6P24.3) MUTATED 57 40 53
AMP PEAK 8(6P24.3) WILD-TYPE 29 44 38

Figure S24.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6p24.3' versus 'MRNASEQ_CNMF'

P value = 0.00677 (Fisher's exact test), Q value = 0.043

Table S25.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
AMP PEAK 8(6P24.3) MUTATED 72 35 52 52
AMP PEAK 8(6P24.3) WILD-TYPE 44 38 53 21

Figure S25.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00421 (Fisher's exact test), Q value = 0.032

Table S26.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
AMP PEAK 8(6P24.3) MUTATED 72 95 44
AMP PEAK 8(6P24.3) WILD-TYPE 33 70 53

Figure S26.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.032

Table S27.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
AMP PEAK 8(6P24.3) MUTATED 48 73 48 33
AMP PEAK 8(6P24.3) WILD-TYPE 49 30 49 21

Figure S27.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S28.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
AMP PEAK 8(6P24.3) MUTATED 91 35 55 21
AMP PEAK 8(6P24.3) WILD-TYPE 41 58 33 17

Figure S28.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0029

Table S29.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
AMP PEAK 8(6P24.3) MUTATED 36 64 93
AMP PEAK 8(6P24.3) WILD-TYPE 49 55 40

Figure S29.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0024

Table S30.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
AMP PEAK 8(6P24.3) MUTATED 17 14 25 51 15 5 39 16 11
AMP PEAK 8(6P24.3) WILD-TYPE 19 10 26 12 23 12 25 13 4

Figure S30.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.067

Table S31.  Gene #9: 'amp_6q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
AMP PEAK 9(6Q12) MUTATED 26 10 20
AMP PEAK 9(6Q12) WILD-TYPE 60 74 71

Figure S31.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.11

Table S32.  Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
AMP PEAK 9(6Q12) MUTATED 35 14 25 4
AMP PEAK 9(6Q12) WILD-TYPE 97 79 63 34

Figure S32.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0055

Table S33.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 10(7P22.1) MUTATED 103 63 43
AMP PEAK 10(7P22.1) WILD-TYPE 51 47 60

Figure S33.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q34' versus 'CN_CNMF'

P value = 0.00192 (Fisher's exact test), Q value = 0.019

Table S34.  Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 11(7Q34) MUTATED 110 63 52
AMP PEAK 11(7Q34) WILD-TYPE 44 47 51

Figure S34.  Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.019

Table S35.  Gene #11: 'amp_7q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
AMP PEAK 11(7Q34) MUTATED 18 13 42 32 23 15 36 20 7
AMP PEAK 11(7Q34) WILD-TYPE 18 11 9 31 15 2 28 9 8

Figure S35.  Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S36.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 12(8Q24.21) MUTATED 91 68 33
AMP PEAK 12(8Q24.21) WILD-TYPE 63 42 70

Figure S36.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S37.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
AMP PEAK 12(8Q24.21) MUTATED 44 59 26 62
AMP PEAK 12(8Q24.21) WILD-TYPE 67 63 8 37

Figure S37.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S38.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
AMP PEAK 12(8Q24.21) MUTATED 51 29 57 55
AMP PEAK 12(8Q24.21) WILD-TYPE 65 44 48 18

Figure S38.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.071

Table S39.  Gene #13: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 13(11Q13.3) MUTATED 40 15 14
AMP PEAK 13(11Q13.3) WILD-TYPE 114 95 89

Figure S39.  Get High-res Image Gene #13: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.1

Table S40.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 14(12Q14.1) MUTATED 30 20 8
AMP PEAK 14(12Q14.1) WILD-TYPE 124 90 95

Figure S40.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.11

Table S41.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
AMP PEAK 14(12Q14.1) MUTATED 1 2 14 9 9 3 14 5 0
AMP PEAK 14(12Q14.1) WILD-TYPE 35 22 37 54 29 14 50 24 15

Figure S41.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S42.  Gene #16: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 16(13Q31.3) MUTATED 51 41 12
AMP PEAK 16(13Q31.3) WILD-TYPE 103 69 91

Figure S42.  Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q31.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S43.  Gene #16: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
AMP PEAK 16(13Q31.3) MUTATED 29 18 11 45
AMP PEAK 16(13Q31.3) WILD-TYPE 82 104 23 54

Figure S43.  Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0012

Table S44.  Gene #16: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
AMP PEAK 16(13Q31.3) MUTATED 24 11 36 33
AMP PEAK 16(13Q31.3) WILD-TYPE 92 62 69 40

Figure S44.  Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.061

Table S45.  Gene #16: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
AMP PEAK 16(13Q31.3) MUTATED 36 34 34
AMP PEAK 16(13Q31.3) WILD-TYPE 69 131 63

Figure S45.  Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.068

Table S46.  Gene #16: 'amp_13q31.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
AMP PEAK 16(13Q31.3) MUTATED 6 3 8 26 13 6 24 6 4
AMP PEAK 16(13Q31.3) WILD-TYPE 30 21 43 37 25 11 40 23 11

Figure S46.  Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.2' versus 'CN_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.022

Table S47.  Gene #17: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 17(15Q26.2) MUTATED 65 32 23
AMP PEAK 17(15Q26.2) WILD-TYPE 89 78 80

Figure S47.  Get High-res Image Gene #17: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0076

Table S48.  Gene #18: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 18(17Q25.3) MUTATED 67 33 22
AMP PEAK 18(17Q25.3) WILD-TYPE 87 77 81

Figure S48.  Get High-res Image Gene #18: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.13

Table S49.  Gene #18: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
AMP PEAK 18(17Q25.3) MUTATED 32 66 24
AMP PEAK 18(17Q25.3) WILD-TYPE 73 99 73

Figure S49.  Get High-res Image Gene #18: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S50.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 19(20Q13.33) MUTATED 100 60 28
AMP PEAK 19(20Q13.33) WILD-TYPE 54 50 75

Figure S50.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.093

Table S51.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
AMP PEAK 19(20Q13.33) MUTATED 53 52 21 61
AMP PEAK 19(20Q13.33) WILD-TYPE 58 70 13 38

Figure S51.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'RPPA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.085

Table S52.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
AMP PEAK 19(20Q13.33) MUTATED 13 33 24 44 15
AMP PEAK 19(20Q13.33) WILD-TYPE 26 45 19 25 17

Figure S52.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.15

Table S53.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
AMP PEAK 19(20Q13.33) MUTATED 55 74 59
AMP PEAK 19(20Q13.33) WILD-TYPE 50 91 38

Figure S53.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_22q13.2' versus 'CN_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.02

Table S54.  Gene #20: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
AMP PEAK 20(22Q13.2) MUTATED 72 52 28
AMP PEAK 20(22Q13.2) WILD-TYPE 82 58 75

Figure S54.  Get High-res Image Gene #20: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q13.2' versus 'METHLYATION_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.15

Table S55.  Gene #20: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
AMP PEAK 20(22Q13.2) MUTATED 45 40 15 51
AMP PEAK 20(22Q13.2) WILD-TYPE 66 82 19 48

Figure S55.  Get High-res Image Gene #20: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_22q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.061

Table S56.  Gene #20: 'amp_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
AMP PEAK 20(22Q13.2) MUTATED 7 7 30 24 14 5 31 15 5
AMP PEAK 20(22Q13.2) WILD-TYPE 29 17 21 39 24 12 33 14 10

Figure S56.  Get High-res Image Gene #20: 'amp_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.04

Table S57.  Gene #21: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 1(1P36.31) MUTATED 43 26 12
DEL PEAK 1(1P36.31) WILD-TYPE 111 84 91

Figure S57.  Get High-res Image Gene #21: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 0.00637 (Fisher's exact test), Q value = 0.042

Table S58.  Gene #21: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 1(1P36.31) MUTATED 21 18 13 29
DEL PEAK 1(1P36.31) WILD-TYPE 90 104 21 70

Figure S58.  Get High-res Image Gene #21: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.11

Table S59.  Gene #21: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 1(1P36.31) MUTATED 30 26 25
DEL PEAK 1(1P36.31) WILD-TYPE 75 139 72

Figure S59.  Get High-res Image Gene #21: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.064

Table S60.  Gene #21: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
DEL PEAK 1(1P36.31) MUTATED 13 23 23 20
DEL PEAK 1(1P36.31) WILD-TYPE 84 80 74 34

Figure S60.  Get High-res Image Gene #21: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p22.1' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0025

Table S61.  Gene #22: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 2(1P22.1) MUTATED 48 37 12
DEL PEAK 2(1P22.1) WILD-TYPE 106 73 91

Figure S61.  Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 0.00404 (Fisher's exact test), Q value = 0.032

Table S62.  Gene #22: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 2(1P22.1) MUTATED 20 29 16 32
DEL PEAK 2(1P22.1) WILD-TYPE 91 93 18 67

Figure S62.  Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.087

Table S63.  Gene #22: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 2(1P22.1) MUTATED 30 10 36 21
DEL PEAK 2(1P22.1) WILD-TYPE 86 63 69 52

Figure S63.  Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.043

Table S64.  Gene #22: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 2(1P22.1) MUTATED 27 33 37
DEL PEAK 2(1P22.1) WILD-TYPE 78 132 60

Figure S64.  Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.15

Table S65.  Gene #22: 'del_1p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
DEL PEAK 2(1P22.1) MUTATED 16 41 35
DEL PEAK 2(1P22.1) WILD-TYPE 69 78 98

Figure S65.  Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.082

Table S66.  Gene #23: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 3(2Q37.3) MUTATED 51 21 21
DEL PEAK 3(2Q37.3) WILD-TYPE 103 89 82

Figure S66.  Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.061

Table S67.  Gene #23: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 3(2Q37.3) MUTATED 38 21 12 22
DEL PEAK 3(2Q37.3) WILD-TYPE 73 101 22 77

Figure S67.  Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.11

Table S68.  Gene #23: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
DEL PEAK 3(2Q37.3) MUTATED 19 16 33
DEL PEAK 3(2Q37.3) WILD-TYPE 67 68 58

Figure S68.  Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.15

Table S69.  Gene #23: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 3(2Q37.3) MUTATED 39 15 19 20
DEL PEAK 3(2Q37.3) WILD-TYPE 77 58 86 53

Figure S69.  Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.018

Table S70.  Gene #23: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 3(2Q37.3) MUTATED 38 41 14
DEL PEAK 3(2Q37.3) WILD-TYPE 67 124 83

Figure S70.  Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.068

Table S71.  Gene #23: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
DEL PEAK 3(2Q37.3) MUTATED 19 37 18 17
DEL PEAK 3(2Q37.3) WILD-TYPE 78 66 79 37

Figure S71.  Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.13

Table S72.  Gene #23: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
DEL PEAK 3(2Q37.3) MUTATED 44 15 23 9
DEL PEAK 3(2Q37.3) WILD-TYPE 88 78 65 29

Figure S72.  Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.1' versus 'CN_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.16

Table S73.  Gene #24: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 4(3P25.1) MUTATED 24 30 17
DEL PEAK 4(3P25.1) WILD-TYPE 130 80 86

Figure S73.  Get High-res Image Gene #24: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.11

Table S74.  Gene #25: 'del_3q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 5(3Q13.31) MUTATED 24 6 14 18
DEL PEAK 5(3Q13.31) WILD-TYPE 92 67 91 55

Figure S74.  Get High-res Image Gene #25: 'del_3q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.16

Table S75.  Gene #25: 'del_3q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
DEL PEAK 5(3Q13.31) MUTATED 14 25 17 4
DEL PEAK 5(3Q13.31) WILD-TYPE 83 78 80 50

Figure S75.  Get High-res Image Gene #25: 'del_3q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 0.16

Table S76.  Gene #26: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 6(4P16.3) MUTATED 30 31 30
DEL PEAK 6(4P16.3) WILD-TYPE 75 134 67

Figure S76.  Get High-res Image Gene #26: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00685 (Fisher's exact test), Q value = 0.043

Table S77.  Gene #27: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 7(4Q34.3) MUTATED 59 30 21
DEL PEAK 7(4Q34.3) WILD-TYPE 95 80 82

Figure S77.  Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.12

Table S78.  Gene #27: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 7(4Q34.3) MUTATED 32 16 43 19
DEL PEAK 7(4Q34.3) WILD-TYPE 84 57 62 54

Figure S78.  Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.034

Table S79.  Gene #27: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 7(4Q34.3) MUTATED 27 41 42
DEL PEAK 7(4Q34.3) WILD-TYPE 78 124 55

Figure S79.  Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.026

Table S80.  Gene #27: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
DEL PEAK 7(4Q34.3) MUTATED 26 38 28 15
DEL PEAK 7(4Q34.3) WILD-TYPE 106 55 60 23

Figure S80.  Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.16

Table S81.  Gene #27: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
DEL PEAK 7(4Q34.3) MUTATED 9 5 17 14 20 8 17 10 3
DEL PEAK 7(4Q34.3) WILD-TYPE 27 19 34 49 18 9 47 19 12

Figure S81.  Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S82.  Gene #28: 'del_5p15.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 8(5P15.31) MUTATED 16 49 14
DEL PEAK 8(5P15.31) WILD-TYPE 138 61 89

Figure S82.  Get High-res Image Gene #28: 'del_5p15.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S83.  Gene #29: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 9(5Q12.1) MUTATED 26 57 14
DEL PEAK 9(5Q12.1) WILD-TYPE 128 53 89

Figure S83.  Get High-res Image Gene #29: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.022

Table S84.  Gene #29: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
DEL PEAK 9(5Q12.1) MUTATED 2 18 11 20 14
DEL PEAK 9(5Q12.1) WILD-TYPE 37 60 32 49 18

Figure S84.  Get High-res Image Gene #29: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S85.  Gene #30: 'del_5q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 10(5Q31.3) MUTATED 33 72 26
DEL PEAK 10(5Q31.3) WILD-TYPE 121 38 77

Figure S85.  Get High-res Image Gene #30: 'del_5q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.3' versus 'METHLYATION_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.12

Table S86.  Gene #30: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 10(5Q31.3) MUTATED 43 42 5 41
DEL PEAK 10(5Q31.3) WILD-TYPE 68 80 29 58

Figure S86.  Get High-res Image Gene #30: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q31.3' versus 'RPPA_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.11

Table S87.  Gene #30: 'del_5q31.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
DEL PEAK 10(5Q31.3) MUTATED 5 26 14 25 15
DEL PEAK 10(5Q31.3) WILD-TYPE 34 52 29 44 17

Figure S87.  Get High-res Image Gene #30: 'del_5q31.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S88.  Gene #31: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 11(6Q21) MUTATED 132 54 28
DEL PEAK 11(6Q21) WILD-TYPE 22 56 75

Figure S88.  Get High-res Image Gene #31: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q21' versus 'METHLYATION_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.018

Table S89.  Gene #31: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 11(6Q21) MUTATED 72 55 19 68
DEL PEAK 11(6Q21) WILD-TYPE 39 67 15 31

Figure S89.  Get High-res Image Gene #31: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q21' versus 'MRNASEQ_CNMF'

P value = 0.00192 (Fisher's exact test), Q value = 0.019

Table S90.  Gene #31: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 11(6Q21) MUTATED 78 29 65 42
DEL PEAK 11(6Q21) WILD-TYPE 38 44 40 31

Figure S90.  Get High-res Image Gene #31: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S91.  Gene #32: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 12(6Q26) MUTATED 135 57 29
DEL PEAK 12(6Q26) WILD-TYPE 19 53 74

Figure S91.  Get High-res Image Gene #32: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00417 (Fisher's exact test), Q value = 0.032

Table S92.  Gene #32: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 12(6Q26) MUTATED 71 59 20 71
DEL PEAK 12(6Q26) WILD-TYPE 40 63 14 28

Figure S92.  Get High-res Image Gene #32: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00634 (Fisher's exact test), Q value = 0.042

Table S93.  Gene #32: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 12(6Q26) MUTATED 78 31 67 45
DEL PEAK 12(6Q26) WILD-TYPE 38 42 38 28

Figure S93.  Get High-res Image Gene #32: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.004

Table S94.  Gene #33: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 13(8P23.3) MUTATED 54 17 18
DEL PEAK 13(8P23.3) WILD-TYPE 100 93 85

Figure S94.  Get High-res Image Gene #33: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'RPPA_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.13

Table S95.  Gene #33: 'del_8p23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
DEL PEAK 13(8P23.3) MUTATED 4 19 10 26 9
DEL PEAK 13(8P23.3) WILD-TYPE 35 59 33 43 23

Figure S95.  Get High-res Image Gene #33: 'del_8p23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_8p23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.1

Table S96.  Gene #33: 'del_8p23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
DEL PEAK 13(8P23.3) MUTATED 27 13 28
DEL PEAK 13(8P23.3) WILD-TYPE 59 71 63

Figure S96.  Get High-res Image Gene #33: 'del_8p23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0025

Table S97.  Gene #34: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 14(9P23) MUTATED 112 84 53
DEL PEAK 14(9P23) WILD-TYPE 42 26 50

Figure S97.  Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.12

Table S98.  Gene #34: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 14(9P23) MUTATED 80 71 23 75
DEL PEAK 14(9P23) WILD-TYPE 31 51 11 24

Figure S98.  Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.15

Table S99.  Gene #34: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
DEL PEAK 14(9P23) MUTATED 24 58 30 38 26
DEL PEAK 14(9P23) WILD-TYPE 15 20 13 31 6

Figure S99.  Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.15

Table S100.  Gene #34: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 14(9P23) MUTATED 77 41 80 51
DEL PEAK 14(9P23) WILD-TYPE 39 32 25 22

Figure S100.  Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.014

Table S101.  Gene #34: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
DEL PEAK 14(9P23) MUTATED 19 18 31 36 27 16 47 17 15
DEL PEAK 14(9P23) WILD-TYPE 17 6 20 27 11 1 17 12 0

Figure S101.  Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S102.  Gene #35: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 15(9P21.3) MUTATED 130 90 58
DEL PEAK 15(9P21.3) WILD-TYPE 24 20 45

Figure S102.  Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0077

Table S103.  Gene #35: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 15(9P21.3) MUTATED 89 78 25 86
DEL PEAK 15(9P21.3) WILD-TYPE 22 44 9 13

Figure S103.  Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 0.00821 (Fisher's exact test), Q value = 0.051

Table S104.  Gene #35: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
DEL PEAK 15(9P21.3) MUTATED 24 65 35 45 28
DEL PEAK 15(9P21.3) WILD-TYPE 15 13 8 24 4

Figure S104.  Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.022

Table S105.  Gene #35: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 15(9P21.3) MUTATED 87 44 89 58
DEL PEAK 15(9P21.3) WILD-TYPE 29 29 16 15

Figure S105.  Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.027

Table S106.  Gene #35: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 15(9P21.3) MUTATED 81 113 84
DEL PEAK 15(9P21.3) WILD-TYPE 24 52 13

Figure S106.  Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.12

Table S107.  Gene #35: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
DEL PEAK 15(9P21.3) MUTATED 66 73 82 43
DEL PEAK 15(9P21.3) WILD-TYPE 31 30 15 11

Figure S107.  Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00262 (Fisher's exact test), Q value = 0.022

Table S108.  Gene #35: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
DEL PEAK 15(9P21.3) MUTATED 23 19 33 41 34 16 51 21 15
DEL PEAK 15(9P21.3) WILD-TYPE 13 5 18 22 4 1 13 8 0

Figure S108.  Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S109.  Gene #36: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 16(10P15.3) MUTATED 90 84 25
DEL PEAK 16(10P15.3) WILD-TYPE 64 26 78

Figure S109.  Get High-res Image Gene #36: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.033

Table S110.  Gene #36: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 16(10P15.3) MUTATED 57 55 19 68
DEL PEAK 16(10P15.3) WILD-TYPE 54 67 15 31

Figure S110.  Get High-res Image Gene #36: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00457 (Fisher's exact test), Q value = 0.033

Table S111.  Gene #36: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 16(10P15.3) MUTATED 52 35 71 41
DEL PEAK 16(10P15.3) WILD-TYPE 64 38 34 32

Figure S111.  Get High-res Image Gene #36: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.012

Table S112.  Gene #36: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 16(10P15.3) MUTATED 57 75 67
DEL PEAK 16(10P15.3) WILD-TYPE 48 90 30

Figure S112.  Get High-res Image Gene #36: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S113.  Gene #37: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 17(10Q21.1) MUTATED 96 93 28
DEL PEAK 17(10Q21.1) WILD-TYPE 58 17 75

Figure S113.  Get High-res Image Gene #37: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.072

Table S114.  Gene #37: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 17(10Q21.1) MUTATED 66 63 17 71
DEL PEAK 17(10Q21.1) WILD-TYPE 45 59 17 28

Figure S114.  Get High-res Image Gene #37: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.13

Table S115.  Gene #37: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 17(10Q21.1) MUTATED 59 90 68
DEL PEAK 17(10Q21.1) WILD-TYPE 46 75 29

Figure S115.  Get High-res Image Gene #37: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S116.  Gene #38: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 18(10Q23.31) MUTATED 103 93 34
DEL PEAK 18(10Q23.31) WILD-TYPE 51 17 69

Figure S116.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.021

Table S117.  Gene #38: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 18(10Q23.31) MUTATED 70 64 20 76
DEL PEAK 18(10Q23.31) WILD-TYPE 41 58 14 23

Figure S117.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.13

Table S118.  Gene #38: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 18(10Q23.31) MUTATED 63 42 73 52
DEL PEAK 18(10Q23.31) WILD-TYPE 53 31 32 21

Figure S118.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.095

Table S119.  Gene #38: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 18(10Q23.31) MUTATED 63 95 72
DEL PEAK 18(10Q23.31) WILD-TYPE 42 70 25

Figure S119.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S120.  Gene #39: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 19(10Q26.3) MUTATED 103 95 38
DEL PEAK 19(10Q26.3) WILD-TYPE 51 15 65

Figure S120.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.029

Table S121.  Gene #39: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 19(10Q26.3) MUTATED 69 69 20 78
DEL PEAK 19(10Q26.3) WILD-TYPE 42 53 14 21

Figure S121.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00642 (Fisher's exact test), Q value = 0.042

Table S122.  Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 19(10Q26.3) MUTATED 62 44 77 53
DEL PEAK 19(10Q26.3) WILD-TYPE 54 29 28 20

Figure S122.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00627 (Fisher's exact test), Q value = 0.042

Table S123.  Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 19(10Q26.3) MUTATED 64 97 75
DEL PEAK 19(10Q26.3) WILD-TYPE 41 68 22

Figure S123.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0055

Table S124.  Gene #40: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 20(11P15.5) MUTATED 50 46 18
DEL PEAK 20(11P15.5) WILD-TYPE 104 64 85

Figure S124.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S125.  Gene #41: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 21(11Q23.3) MUTATED 101 67 36
DEL PEAK 21(11Q23.3) WILD-TYPE 53 43 67

Figure S125.  Get High-res Image Gene #41: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.16

Table S126.  Gene #41: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
DEL PEAK 21(11Q23.3) MUTATED 45 61 87
DEL PEAK 21(11Q23.3) WILD-TYPE 40 58 46

Figure S126.  Get High-res Image Gene #41: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q23.3' versus 'CN_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.12

Table S127.  Gene #42: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 22(12Q23.3) MUTATED 44 32 16
DEL PEAK 22(12Q23.3) WILD-TYPE 110 78 87

Figure S127.  Get High-res Image Gene #42: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q23.3' versus 'METHLYATION_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.059

Table S128.  Gene #42: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 22(12Q23.3) MUTATED 38 21 5 28
DEL PEAK 22(12Q23.3) WILD-TYPE 73 101 29 71

Figure S128.  Get High-res Image Gene #42: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S129.  Gene #44: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 24(14Q23.3) MUTATED 58 45 17
DEL PEAK 24(14Q23.3) WILD-TYPE 96 65 86

Figure S129.  Get High-res Image Gene #44: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.072

Table S130.  Gene #44: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
DEL PEAK 24(14Q23.3) MUTATED 37 19 26
DEL PEAK 24(14Q23.3) WILD-TYPE 49 65 65

Figure S130.  Get High-res Image Gene #44: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00602 (Fisher's exact test), Q value = 0.041

Table S131.  Gene #44: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 24(14Q23.3) MUTATED 28 26 47 19
DEL PEAK 24(14Q23.3) WILD-TYPE 88 47 58 54

Figure S131.  Get High-res Image Gene #44: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.12

Table S132.  Gene #44: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 24(14Q23.3) MUTATED 28 50 42
DEL PEAK 24(14Q23.3) WILD-TYPE 77 115 55

Figure S132.  Get High-res Image Gene #44: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S133.  Gene #45: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 25(14Q32.31) MUTATED 57 44 16
DEL PEAK 25(14Q32.31) WILD-TYPE 97 66 87

Figure S133.  Get High-res Image Gene #45: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.12

Table S134.  Gene #45: 'del_14q32.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
DEL PEAK 25(14Q32.31) MUTATED 37 21 26
DEL PEAK 25(14Q32.31) WILD-TYPE 49 63 65

Figure S134.  Get High-res Image Gene #45: 'del_14q32.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.064

Table S135.  Gene #45: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 25(14Q32.31) MUTATED 28 24 46 19
DEL PEAK 25(14Q32.31) WILD-TYPE 88 49 59 54

Figure S135.  Get High-res Image Gene #45: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.1

Table S136.  Gene #45: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 25(14Q32.31) MUTATED 29 46 42
DEL PEAK 25(14Q32.31) WILD-TYPE 76 119 55

Figure S136.  Get High-res Image Gene #45: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'RPPA_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.1

Table S137.  Gene #46: 'del_15q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
DEL PEAK 26(15Q13.3) MUTATED 4 16 11 25 5
DEL PEAK 26(15Q13.3) WILD-TYPE 35 62 32 44 27

Figure S137.  Get High-res Image Gene #46: 'del_15q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.15

Table S138.  Gene #46: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 26(15Q13.3) MUTATED 33 30 21
DEL PEAK 26(15Q13.3) WILD-TYPE 72 135 76

Figure S138.  Get High-res Image Gene #46: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00832 (Fisher's exact test), Q value = 0.051

Table S139.  Gene #46: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
DEL PEAK 26(15Q13.3) MUTATED 10 34 35
DEL PEAK 26(15Q13.3) WILD-TYPE 75 85 98

Figure S139.  Get High-res Image Gene #46: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.16

Table S140.  Gene #47: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 27(15Q21.1) MUTATED 46 28 17
DEL PEAK 27(15Q21.1) WILD-TYPE 108 82 86

Figure S140.  Get High-res Image Gene #47: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.11

Table S141.  Gene #47: 'del_15q21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
DEL PEAK 27(15Q21.1) MUTATED 30 14 26
DEL PEAK 27(15Q21.1) WILD-TYPE 56 70 65

Figure S141.  Get High-res Image Gene #47: 'del_15q21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.00966 (Fisher's exact test), Q value = 0.057

Table S142.  Gene #48: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 28(16P13.3) MUTATED 37 12 13
DEL PEAK 28(16P13.3) WILD-TYPE 117 98 90

Figure S142.  Get High-res Image Gene #48: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.00909 (Fisher's exact test), Q value = 0.055

Table S143.  Gene #48: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 28(16P13.3) MUTATED 26 16 10 10
DEL PEAK 28(16P13.3) WILD-TYPE 85 106 24 89

Figure S143.  Get High-res Image Gene #48: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.16

Table S144.  Gene #48: 'del_16p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
DEL PEAK 28(16P13.3) MUTATED 22 10 13
DEL PEAK 28(16P13.3) WILD-TYPE 64 74 78

Figure S144.  Get High-res Image Gene #48: 'del_16p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S145.  Gene #49: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 29(16Q12.1) MUTATED 78 16 23
DEL PEAK 29(16Q12.1) WILD-TYPE 76 94 80

Figure S145.  Get High-res Image Gene #49: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S146.  Gene #50: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 30(16Q23.1) MUTATED 79 16 25
DEL PEAK 30(16Q23.1) WILD-TYPE 75 94 78

Figure S146.  Get High-res Image Gene #50: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.15

Table S147.  Gene #50: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 30(16Q23.1) MUTATED 47 34 13 26
DEL PEAK 30(16Q23.1) WILD-TYPE 64 88 21 73

Figure S147.  Get High-res Image Gene #50: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.087

Table S148.  Gene #50: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 30(16Q23.1) MUTATED 48 23 23 26
DEL PEAK 30(16Q23.1) WILD-TYPE 68 50 82 47

Figure S148.  Get High-res Image Gene #50: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S149.  Gene #51: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 31(16Q24.3) MUTATED 85 19 29
DEL PEAK 31(16Q24.3) WILD-TYPE 69 91 74

Figure S149.  Get High-res Image Gene #51: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.3' versus 'RPPA_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.15

Table S150.  Gene #51: 'del_16q24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 78 43 69 32
DEL PEAK 31(16Q24.3) MUTATED 9 25 22 30 9
DEL PEAK 31(16Q24.3) WILD-TYPE 30 53 21 39 23

Figure S150.  Get High-res Image Gene #51: 'del_16q24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.11

Table S151.  Gene #51: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 31(16Q24.3) MUTATED 52 25 27 29
DEL PEAK 31(16Q24.3) WILD-TYPE 64 48 78 44

Figure S151.  Get High-res Image Gene #51: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.11

Table S152.  Gene #51: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 31(16Q24.3) MUTATED 38 70 25
DEL PEAK 31(16Q24.3) WILD-TYPE 67 95 72

Figure S152.  Get High-res Image Gene #51: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.13

Table S153.  Gene #52: 'del_17p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 84 91
DEL PEAK 32(17P13.3) MUTATED 28 43 33
DEL PEAK 32(17P13.3) WILD-TYPE 58 41 58

Figure S153.  Get High-res Image Gene #52: 'del_17p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.072

Table S154.  Gene #53: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 33(19P13.3) MUTATED 50 36 18
DEL PEAK 33(19P13.3) WILD-TYPE 104 74 85

Figure S154.  Get High-res Image Gene #53: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0025

Table S155.  Gene #53: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 33(19P13.3) MUTATED 51 16 18 19
DEL PEAK 33(19P13.3) WILD-TYPE 65 57 87 54

Figure S155.  Get High-res Image Gene #53: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.12

Table S156.  Gene #54: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 110 103
DEL PEAK 34(XP21.1) MUTATED 34 35 17
DEL PEAK 34(XP21.1) WILD-TYPE 120 75 86

Figure S156.  Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S157.  Gene #54: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 111 122 34 99
DEL PEAK 34(XP21.1) MUTATED 38 12 11 25
DEL PEAK 34(XP21.1) WILD-TYPE 73 110 23 74

Figure S157.  Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.00931 (Fisher's exact test), Q value = 0.056

Table S158.  Gene #54: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 73 105 73
DEL PEAK 34(XP21.1) MUTATED 34 7 27 18
DEL PEAK 34(XP21.1) WILD-TYPE 82 66 78 55

Figure S158.  Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0042 (Fisher's exact test), Q value = 0.032

Table S159.  Gene #54: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 165 97
DEL PEAK 34(XP21.1) MUTATED 34 26 26
DEL PEAK 34(XP21.1) WILD-TYPE 71 139 71

Figure S159.  Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.021

Table S160.  Gene #54: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 103 97 54
DEL PEAK 34(XP21.1) MUTATED 22 37 16 7
DEL PEAK 34(XP21.1) WILD-TYPE 75 66 81 47

Figure S160.  Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.095

Table S161.  Gene #54: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 93 88 38
DEL PEAK 34(XP21.1) MUTATED 39 15 24 4
DEL PEAK 34(XP21.1) WILD-TYPE 93 78 64 34

Figure S161.  Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.15

Table S162.  Gene #54: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 119 133
DEL PEAK 34(XP21.1) MUTATED 16 21 40
DEL PEAK 34(XP21.1) WILD-TYPE 69 98 93

Figure S162.  Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0088

Table S163.  Gene #54: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 36 24 51 63 38 17 64 29 15
DEL PEAK 34(XP21.1) MUTATED 6 8 8 23 3 9 11 4 5
DEL PEAK 34(XP21.1) WILD-TYPE 30 16 43 40 35 8 53 25 10

Figure S163.  Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/22533834/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/22546664/SKCM-TM.transferedmergedcluster.txt

  • Number of patients = 367

  • Number of significantly focal cnvs = 54

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, 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.

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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