Correlation between copy number variation genes (focal events) and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1M907Z6
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1M907Z6
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 71 focal events and 14 molecular subtypes across 579 patients, 267 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p34.3 cnv correlated to 'CN_CNMF'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_1q42.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_2p23.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_2q31.2 cnv correlated to 'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • amp_3q26.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • amp_4p16.3 cnv correlated to 'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_4q13.3 cnv correlated to 'CN_CNMF'.

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

  • amp_6p22.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • amp_7q36.3 cnv correlated to 'CN_CNMF'.

  • amp_8p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • amp_8q24.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_11q14.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_12p13.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_12p12.1 cnv correlated to 'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q15 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_14q11.2 cnv correlated to 'MRNA_CNMF' and 'MIR_CHIERARCHICAL'.

  • amp_14q32.33 cnv correlated to 'MIR_CHIERARCHICAL' and 'CN_CNMF'.

  • amp_15q26.3 cnv correlated to 'CN_CNMF'.

  • amp_17q25.3 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • amp_18q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_19p13.12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • amp_19q12 cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • amp_19q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20p13 cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_20q13.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_22q12.2 cnv correlated to 'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_xp11.23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_xq28 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_1p36.11 cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'RPPA_CNMF'.

  • del_1q41 cnv correlated to 'CN_CNMF'.

  • del_2q22.1 cnv correlated to 'MIR_CHIERARCHICAL'.

  • del_2q37.3 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3p26.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_4q22.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_4q34.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_5q13.2 cnv correlated to 'CN_CNMF'.

  • del_6q27 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_7p22.1 cnv correlated to 'CN_CNMF'.

  • del_8p23.3 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • del_8p21.2 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • del_9p24.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_9q34.13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_10q24.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_11p15.5 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_12q24.33 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q23.3 cnv correlated to 'CN_CNMF'.

  • del_15q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_15q15.1 cnv correlated to 'MRNA_CNMF',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_16p13.3 cnv correlated to 'MIR_CHIERARCHICAL' and 'RPPA_CNMF'.

  • del_16q22.1 cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_18q23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • del_19q13.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_19q13.43 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_21q22.3 cnv correlated to 'MRNA_CHIERARCHICAL'.

  • del_22q13.32 cnv correlated to 'MIR_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_xp21.1 cnv correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 71 focal events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 267 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 20q13 33 402 (69%) 177 0.0104
(0.0657) 		0.00074
(0.00826) 		0.684
(0.838) 		0.0014
(0.0143) 		1e-05
(0.000226) 		1e-05
(0.000226) 		0.347
(0.604) 		0.966
(1.00) 		0.0254
(0.122) 		0.00248
(0.0226) 		0.476
(0.722) 		0.0495
(0.185) 		0.624
(0.82) 		0.0143
(0.0838)
del 13q14 2 364 (63%) 215 0.00956
(0.0605) 		0.0161
(0.0903) 		0.609
(0.816) 		0.0418
(0.169) 		0.00024
(0.00331) 		4e-05
(0.00075) 		0.00114
(0.0119) 		0.00293
(0.0245) 		0.0198
(0.102) 		0.0441
(0.173) 		0.376
(0.63) 		0.368
(0.627) 		0.675
(0.833) 		0.251
(0.501)
del 15q11 2 299 (52%) 280 0.00613
(0.0426) 		0.0369
(0.153) 		0.0108
(0.0673) 		0.00593
(0.0415) 		1e-05
(0.000226) 		4e-05
(0.00075) 		0.144
(0.361) 		0.499
(0.743) 		0.00052
(0.00654) 		0.192
(0.424) 		0.0251
(0.122) 		0.00956
(0.0605) 		1
(1.00) 		0.372
(0.628)
del 19q13 33 299 (52%) 280 0.00019
(0.00278) 		0.00223
(0.0211) 		0.0469
(0.179) 		0.0205
(0.105) 		0.0141
(0.0828) 		0.00239
(0.0222) 		0.0759
(0.246) 		0.0323
(0.141) 		0.0155
(0.0885) 		0.0164
(0.0903) 		0.321
(0.574) 		0.129
(0.329) 		0.391
(0.641) 		0.114
(0.307)
amp 19p13 12 315 (54%) 264 0.0002
(0.00284) 		0.00021
(0.00294) 		0.039
(0.161) 		0.251
(0.501) 		1e-05
(0.000226) 		1e-05
(0.000226) 		8e-05
(0.00128) 		0.00143
(0.0145) 		0.0419
(0.169) 		0.186
(0.414) 		0.589
(0.806) 		0.0974
(0.284) 		1
(1.00) 		0.476
(0.722)
amp 20q11 21 348 (60%) 231 0.00255
(0.0226) 		0.00308
(0.0252) 		0.112
(0.303) 		0.00324
(0.026) 		1e-05
(0.000226) 		1e-05
(0.000226) 		0.0853
(0.266) 		0.177
(0.4) 		0.00332
(0.0264) 		0.00259
(0.0226) 		0.288
(0.536) 		0.0007
(0.008) 		1
(1.00) 		0.333
(0.584)
del 12q24 33 220 (38%) 359 0.00116
(0.012) 		0.0986
(0.285) 		0.163
(0.383) 		0.014
(0.0828) 		1e-05
(0.000226) 		0.0192
(0.0997) 		0.147
(0.364) 		0.403
(0.654) 		0.0492
(0.185) 		0.0262
(0.125) 		0.0156
(0.0889) 		0.005
(0.0365) 		0.646
(0.832) 		1
(1.00)
amp 8q24 21 461 (80%) 118 1e-05
(0.000226) 		1e-05
(0.000226) 		0.25
(0.501) 		0.00283
(0.024) 		1e-05
(0.000226) 		0.00445
(0.0335) 		0.667
(0.833) 		0.0765
(0.246) 		1e-05
(0.000226) 		1e-05
(0.000226) 		0.162
(0.383) 		0.0983
(0.285) 		0.571
(0.798) 		0.573
(0.798)
amp 12p12 1 313 (54%) 266 0.126
(0.326) 		0.307
(0.559) 		0.9
(0.987) 		0.0411
(0.168) 		1e-05
(0.000226) 		5e-05
(0.000857) 		0.176
(0.4) 		0.606
(0.816) 		0.00489
(0.036) 		0.00419
(0.0318) 		0.448
(0.7) 		0.00532
(0.0383) 		0.391
(0.641) 		0.0441
(0.173)
amp 20p13 317 (55%) 262 0.188
(0.417) 		0.00538
(0.0385) 		0.208
(0.445) 		0.0333
(0.142) 		1e-05
(0.000226) 		1e-05
(0.000226) 		0.567
(0.794) 		0.361
(0.621) 		0.015
(0.087) 		0.0448
(0.174) 		0.249
(0.501) 		0.00068
(0.00786) 		1
(1.00) 		0.936
(1.00)
del 3p26 2 209 (36%) 370 0.155
(0.374) 		0.00062
(0.00742) 		0.00624
(0.0431) 		0.00472
(0.035) 		5e-05
(0.000857) 		0.00058
(0.00712) 		0.384
(0.636) 		0.105
(0.294) 		0.00085
(0.00908) 		0.00093
(0.00983) 		0.632
(0.822) 		0.124
(0.324) 		0.415
(0.666) 		0.94
(1.00)
del 9q34 13 342 (59%) 237 0.0174
(0.0939) 		0.00082
(0.00886) 		0.698
(0.846) 		0.407
(0.657) 		1e-05
(0.000226) 		0.0176
(0.0943) 		0.684
(0.838) 		0.0463
(0.178) 		0.0999
(0.285) 		0.00871
(0.0565) 		0.0496
(0.185) 		0.102
(0.289) 		1
(1.00) 		0.789
(0.915)
del 10q24 2 251 (43%) 328 0.00315
(0.0255) 		0.00232
(0.0218) 		0.00689
(0.0466) 		0.235
(0.482) 		5e-05
(0.000857) 		0.002
(0.0191) 		0.297
(0.55) 		0.0326
(0.141) 		0.783
(0.911) 		0.668
(0.833) 		0.00159
(0.0158) 		0.365
(0.625) 		1
(1.00) 		0.782
(0.911)
del 15q15 1 363 (63%) 216 0.0258
(0.123) 		0.0594
(0.206) 		0.0218
(0.11) 		0.00252
(0.0226) 		1e-05
(0.000226) 		1e-05
(0.000226) 		0.059
(0.206) 		0.22
(0.462) 		0.0164
(0.0903) 		0.374
(0.63) 		0.394
(0.643) 		0.00184
(0.0179) 		0.204
(0.443) 		0.145
(0.363)
amp 1q42 2 322 (56%) 257 0.0239
(0.118) 		0.0268
(0.125) 		0.885
(0.978) 		0.0082
(0.0536) 		1e-05
(0.000226) 		7e-05
(0.00114) 		0.107
(0.296) 		0.805
(0.927) 		0.0858
(0.266) 		0.064
(0.217) 		0.266
(0.517) 		0.00287
(0.0242) 		1
(1.00) 		0.512
(0.75)
amp 11q14 1 257 (44%) 322 0.00521
(0.0378) 		0.00375
(0.0291) 		0.774
(0.909) 		0.307
(0.559) 		2e-05
(0.000432) 		0.00257
(0.0226) 		0.426
(0.672) 		0.619
(0.82) 		0.308
(0.559) 		0.0187
(0.098) 		0.131
(0.336) 		0.921
(0.994) 		0.0427
(0.169) 		0.435
(0.682)
amp 12p13 33 330 (57%) 249 0.0239
(0.118) 		0.00309
(0.0252) 		0.264
(0.516) 		0.0545
(0.196) 		1e-05
(0.000226) 		0.0002
(0.00284) 		0.125
(0.325) 		0.301
(0.553) 		0.0187
(0.098) 		0.148
(0.365) 		0.534
(0.764) 		0.00778
(0.0514) 		0.378
(0.631) 		0.528
(0.761)
amp 12q15 222 (38%) 357 0.0027
(0.0231) 		0.244
(0.495) 		0.577
(0.8) 		0.00251
(0.0226) 		1e-05
(0.000226) 		5e-05
(0.000857) 		0.0677
(0.225) 		0.62
(0.82) 		0.0111
(0.0688) 		0.00247
(0.0226) 		0.969
(1.00) 		0.102
(0.289) 		0.231
(0.475) 		0.269
(0.518)
amp 1q21 3 367 (63%) 212 0.268
(0.517) 		0.163
(0.383) 		0.641
(0.831) 		0.398
(0.647) 		1e-05
(0.000226) 		0.00014
(0.00214) 		0.0265
(0.125) 		0.0137
(0.0814) 		0.567
(0.794) 		0.117
(0.313) 		0.843
(0.95) 		0.00587
(0.0414) 		0.652
(0.833) 		0.693
(0.844)
amp 2p23 2 252 (44%) 327 0.33
(0.581) 		0.0128
(0.0775) 		0.759
(0.898) 		0.171
(0.391) 		1e-05
(0.000226) 		0.00452
(0.0338) 		0.159
(0.378) 		0.477
(0.722) 		0.034
(0.144) 		0.00053
(0.00659) 		0.92
(0.994) 		0.202
(0.441) 		1
(1.00) 		0.67
(0.833)
amp 2q31 2 262 (45%) 317 0.115
(0.308) 		0.171
(0.391) 		0.0332
(0.142) 		0.0292
(0.131) 		1e-05
(0.000226) 		0.00765
(0.051) 		0.0282
(0.129) 		0.92
(0.994) 		0.171
(0.391) 		0.12
(0.317) 		0.289
(0.537) 		0.0855
(0.266) 		0.67
(0.833) 		0.889
(0.981)
amp 19q12 322 (56%) 257 0.122
(0.322) 		0.00656
(0.045) 		0.0286
(0.129) 		0.513
(0.75) 		1e-05
(0.000226) 		1e-05
(0.000226) 		0.0118
(0.0724) 		0.803
(0.926) 		0.607
(0.816) 		0.232
(0.477) 		0.347
(0.604) 		0.0584
(0.205) 		1
(1.00) 		0.781
(0.911)
amp 22q12 2 91 (16%) 488 0.624
(0.82) 		0.155
(0.374) 		0.0716
(0.235) 		0.0342
(0.145) 		0.00762
(0.051) 		0.00081
(0.00885) 		0.675
(0.833) 		0.00154
(0.0155) 		0.156
(0.375) 		0.0762
(0.246) 		0.109
(0.3) 		0.0147
(0.0855) 		1
(1.00) 		0.0865
(0.266)
del 2q37 3 175 (30%) 404 0.0162
(0.0903) 		0.462
(0.714) 		0.631
(0.822) 		0.0274
(0.127) 		4e-05
(0.00075) 		0.0875
(0.266) 		0.91
(0.991) 		0.38
(0.633) 		0.125
(0.325) 		0.355
(0.613) 		0.0239
(0.118) 		0.0193
(0.1) 		0.323
(0.574) 		0.965
(1.00)
del 6q27 380 (66%) 199 0.318
(0.573) 		0.0618
(0.212) 		0.273
(0.518) 		0.103
(0.292) 		1e-05
(0.000226) 		5e-05
(0.000857) 		0.915
(0.994) 		0.9
(0.987) 		0.00076
(0.00839) 		0.00181
(0.0178) 		0.562
(0.79) 		0.0242
(0.118) 		0.691
(0.844) 		0.431
(0.68)
del 9p24 3 261 (45%) 318 0.00025
(0.00336) 		4e-05
(0.00075) 		0.619
(0.82) 		0.0134
(0.0802) 		0.0619
(0.212) 		6e-05
(0.000994) 		0.454
(0.705) 		0.167
(0.385) 		0.0234
(0.117) 		0.232
(0.477) 		0.087
(0.266) 		0.125
(0.325) 		1
(1.00) 		0.512
(0.75)
del 19q13 43 285 (49%) 294 0.0163
(0.0903) 		0.082
(0.26) 		0.0794
(0.253) 		0.387
(0.64) 		0.00011
(0.00171) 		3e-05
(0.000609) 		0.177
(0.4) 		0.398
(0.647) 		0.545
(0.771) 		0.0601
(0.208) 		0.518
(0.753) 		0.119
(0.315) 		0.0427
(0.169) 		0.0215
(0.109)
del 22q13 32 503 (87%) 76 0.206
(0.445) 		0.124
(0.324) 		0.0334
(0.142) 		0.287
(0.535) 		0.0173
(0.0939) 		0.159
(0.378) 		0.038
(0.157) 		0.0427
(0.169) 		0.0903
(0.27) 		0.0785
(0.251) 		0.0366
(0.153) 		0.576
(0.8)
amp 3q26 2 485 (84%) 94 0.00897
(0.0575) 		0.0254
(0.122) 		0.817
(0.935) 		0.278
(0.522) 		1e-05
(0.000226) 		0.0361
(0.152) 		0.898
(0.987) 		0.0547
(0.196) 		0.148
(0.365) 		0.441
(0.69) 		0.124
(0.324) 		0.067
(0.224) 		1
(1.00) 		0.578
(0.8)
amp 4p16 3 160 (28%) 419 1
(1.00) 		0.32
(0.574) 		0.029
(0.13) 		0.48
(0.724) 		0.0004
(0.0051) 		0.0269
(0.125) 		0.238
(0.485) 		0.475
(0.722) 		0.367
(0.626) 		0.693
(0.844) 		0.627
(0.82) 		0.0181
(0.0961) 		0.652
(0.833) 		0.578
(0.8)
del 4q34 3 421 (73%) 158 0.0533
(0.194) 		0.00071
(0.00802) 		0.0622
(0.212) 		0.0283
(0.129) 		0.185
(0.413) 		0.58
(0.8) 		0.838
(0.948) 		0.167
(0.385) 		0.0295
(0.132) 		0.0461
(0.178) 		0.42
(0.67) 		0.53
(0.762) 		1
(1.00) 		0.561
(0.79)
amp 5p15 33 309 (53%) 270 1
(1.00) 		0.0546
(0.196) 		0.628
(0.821) 		0.25
(0.501) 		1e-05
(0.000226) 		0.0976
(0.284) 		0.518
(0.753) 		0.156
(0.375) 		0.781
(0.911) 		0.028
(0.129) 		0.0242
(0.118) 		0.146
(0.364) 		0.231
(0.475) 		0.27
(0.518)
amp 6p22 3 306 (53%) 273 0.173
(0.395) 		0.0321
(0.14) 		0.276
(0.52) 		0.0745
(0.242) 		1e-05
(0.000226) 		0.0124
(0.0757) 		0.215
(0.457) 		0.582
(0.8) 		0.239
(0.487) 		0.147
(0.364) 		0.374
(0.63) 		0.613
(0.817) 		1
(1.00) 		0.255
(0.505)
amp 8p11 21 211 (36%) 368 0.11
(0.3) 		0.352
(0.609) 		0.0997
(0.285) 		0.531
(0.763) 		3e-05
(0.000609) 		0.0158
(0.0891) 		0.0494
(0.185) 		0.353
(0.609) 		0.143
(0.361) 		0.274
(0.518) 		0.768
(0.905) 		0.326
(0.575) 		0.231
(0.475) 		0.858
(0.963)
amp 10p15 3 252 (44%) 327 0.823
(0.939) 		0.0995
(0.285) 		0.0544
(0.196) 		0.165
(0.384) 		1e-05
(0.000226) 		0.0006
(0.00727) 		0.412
(0.663) 		0.986
(1.00) 		0.0286
(0.129) 		0.097
(0.284) 		0.377
(0.63) 		0.0667
(0.223) 		1
(1.00) 		0.61
(0.816)
amp 17q25 3 215 (37%) 364 0.472
(0.722) 		0.057
(0.202) 		0.981
(1.00) 		0.665
(0.833) 		0.00398
(0.0307) 		0.773
(0.909) 		0.468
(0.719) 		0.0129
(0.0775) 		0.0268
(0.125) 		0.363
(0.623) 		0.324
(0.574) 		0.128
(0.328) 		1
(1.00) 		0.711
(0.856)
amp 19q13 2 245 (42%) 334 0.945
(1.00) 		0.542
(0.771) 		0.661
(0.833) 		0.391
(0.641) 		1e-05
(0.000226) 		9e-05
(0.00142) 		0.0532
(0.194) 		0.466
(0.717) 		0.544
(0.771) 		0.0268
(0.125) 		0.978
(1.00) 		0.549
(0.775) 		0.675
(0.833) 		0.614
(0.817)
amp xp11 23 159 (27%) 420 0.663
(0.833) 		0.866
(0.969) 		0.418
(0.669) 		0.631
(0.822) 		1e-05
(0.000226) 		0.00191
(0.0184) 		0.583
(0.801) 		0.451
(0.703) 		0.663
(0.833) 		0.682
(0.838) 		0.275
(0.519) 		0.0312
(0.137) 		0.675
(0.833) 		0.632
(0.822)
del 1p36 11 269 (46%) 310 0.738
(0.877) 		0.069
(0.228) 		0.03
(0.133) 		0.115
(0.308) 		6e-05
(0.000994) 		0.0878
(0.266) 		0.0495
(0.185) 		0.207
(0.445) 		0.132
(0.337) 		0.195
(0.429) 		0.221
(0.462) 		0.167
(0.385) 		0.675
(0.833) 		0.978
(1.00)
del 8p23 3 388 (67%) 191 0.0444
(0.173) 		0.15
(0.367) 		0.58
(0.8) 		0.0113
(0.0699) 		1e-05
(0.000226) 		0.0511
(0.189) 		0.842
(0.95) 		0.115
(0.308) 		0.738
(0.877) 		0.903
(0.987) 		0.249
(0.501) 		0.25
(0.501) 		1
(1.00)
del 8p21 2 406 (70%) 173 0.0412
(0.168) 		0.0908
(0.271) 		0.18
(0.404) 		0.00554
(0.0393) 		1e-05
(0.000226) 		0.149
(0.365) 		0.782
(0.911) 		0.702
(0.85) 		0.246
(0.498) 		0.683
(0.838) 		0.579
(0.8) 		0.513
(0.75) 		1
(1.00)
del 11p15 5 346 (60%) 233 0.111
(0.3) 		0.972
(1.00) 		0.619
(0.82) 		0.0873
(0.266) 		1e-05
(0.000226) 		0.00781
(0.0514) 		0.0815
(0.259) 		0.66
(0.833) 		0.892
(0.983) 		0.488
(0.732) 		0.107
(0.296) 		0.00875
(0.0565) 		0.204
(0.443) 		0.928
(0.996)
del 16q22 1 461 (80%) 118 0.497
(0.742) 		0.703
(0.85) 		0.0329
(0.142) 		0.453
(0.705) 		0.00064
(0.00748) 		0.644
(0.832) 		0.342
(0.597) 		0.0502
(0.186) 		0.281
(0.526) 		0.911
(0.991) 		0.31
(0.562) 		0.0472
(0.18) 		1
(1.00) 		0.384
(0.636)
del 19p13 3 512 (88%) 67 0.16
(0.379) 		0.091
(0.271) 		0.837
(0.948) 		0.545
(0.771) 		0.00036
(0.00465) 		0.0178
(0.0951) 		0.0041
(0.0313) 		0.16
(0.38) 		0.47
(0.719) 		0.0549
(0.196) 		0.476
(0.722) 		0.729
(0.871) 		1
(1.00)
amp 14q11 2 148 (26%) 431 0.0167
(0.0915) 		0.0594
(0.206) 		0.29
(0.537) 		0.00679
(0.0462) 		0.069
(0.228) 		0.191
(0.424) 		0.974
(1.00) 		0.204
(0.443) 		0.208
(0.445) 		0.274
(0.518) 		0.3
(0.551) 		0.822
(0.938) 		0.323
(0.574) 		0.278
(0.522)
amp 14q32 33 156 (27%) 423 0.438
(0.687) 		0.653
(0.833) 		0.197
(0.431) 		0.0183
(0.0968) 		0.00015
(0.00223) 		0.29
(0.537) 		0.91
(0.991) 		0.811
(0.931) 		0.178
(0.401) 		0.0916
(0.272) 		0.374
(0.63) 		0.423
(0.672) 		0.0964
(0.283) 		0.139
(0.353)
amp 18q11 2 143 (25%) 436 0.82
(0.938) 		0.78
(0.911) 		0.952
(1.00) 		0.219
(0.462) 		1e-05
(0.000226) 		0.00375
(0.0291) 		0.145
(0.363) 		0.882
(0.978) 		0.538
(0.768) 		0.614
(0.817) 		0.147
(0.364) 		0.513
(0.75) 		0.381
(0.633) 		0.0925
(0.274)
amp xq28 220 (38%) 359 0.247
(0.499) 		0.847
(0.952) 		0.556
(0.784) 		0.121
(0.319) 		0.00035
(0.00458) 		0.177
(0.4) 		0.534
(0.764) 		0.424
(0.672) 		0.601
(0.812) 		0.375
(0.63) 		0.88
(0.978) 		0.808
(0.928) 		0.0427
(0.169) 		0.623
(0.82)
del 3q13 31 84 (15%) 495 0.325
(0.575) 		0.228
(0.474) 		0.567
(0.794) 		0.627
(0.82) 		0.109
(0.3) 		0.0824
(0.26) 		0.235
(0.482) 		0.0368
(0.153) 		0.0438
(0.173) 		0.0879
(0.266) 		0.521
(0.756) 		0.525
(0.76) 		1
(1.00)
del 4q22 1 394 (68%) 185 0.0522
(0.192) 		0.0233
(0.117) 		1
(1.00) 		0.164
(0.384) 		0.0154
(0.0885) 		0.224
(0.467) 		0.0628
(0.214) 		0.917
(0.994) 		0.67
(0.833) 		0.723
(0.867) 		0.308
(0.559) 		0.253
(0.502) 		0.675
(0.833) 		0.411
(0.663)
del 5q12 1 355 (61%) 224 0.884
(0.978) 		0.872
(0.974) 		0.582
(0.8) 		0.0557
(0.198) 		1e-05
(0.000226) 		0.00025
(0.00336) 		0.761
(0.898) 		0.793
(0.918) 		0.203
(0.443) 		0.31
(0.562) 		0.161
(0.381) 		0.255
(0.505) 		1
(1.00) 		0.265
(0.516)
del 16p13 3 313 (54%) 266 0.604
(0.815) 		0.0709
(0.234) 		0.273
(0.518) 		0.0298
(0.132) 		0.107
(0.296) 		0.421
(0.671) 		0.0422
(0.169) 		0.452
(0.704) 		0.827
(0.941) 		0.989
(1.00) 		0.222
(0.464) 		0.485
(0.73) 		0.675
(0.833) 		0.785
(0.912)
del 16q23 1 452 (78%) 127 0.11
(0.3) 		0.245
(0.498) 		0.102
(0.289) 		0.0613
(0.212) 		0.00015
(0.00223) 		0.536
(0.765) 		0.479
(0.724) 		0.371
(0.628) 		0.0968
(0.284) 		0.41
(0.662) 		0.0573
(0.202) 		0.0497
(0.185) 		1
(1.00) 		0.903
(0.987)
del 17q11 2 472 (82%) 107 0.922
(0.994) 		0.192
(0.424) 		0.734
(0.877) 		0.217
(0.459) 		0.00064
(0.00748) 		0.00302
(0.025) 		0.67
(0.833) 		0.512
(0.75) 		0.527
(0.76) 		0.517
(0.753) 		0.149
(0.366) 		0.164
(0.383) 		1
(1.00) 		0.339
(0.594)
del 18q23 381 (66%) 198 0.885
(0.978) 		0.853
(0.958) 		0.371
(0.628) 		0.956
(1.00) 		0.00262
(0.0226) 		0.588
(0.806) 		0.22
(0.462) 		0.275
(0.519) 		0.544
(0.771) 		0.0466
(0.179) 		0.663
(0.833) 		0.492
(0.736) 		0.646
(0.832) 		0.793
(0.918)
amp 1p34 3 292 (50%) 287 0.433
(0.681) 		0.0832
(0.262) 		0.127
(0.328) 		0.0856
(0.266) 		1e-05
(0.000226) 		0.192
(0.424) 		0.273
(0.518) 		0.366
(0.626) 		0.587
(0.805) 		0.758
(0.897) 		0.0878
(0.266) 		0.165
(0.384) 		0.0743
(0.242) 		0.927
(0.996)
amp 4q13 3 113 (20%) 466 0.905
(0.988) 		0.459
(0.71) 		0.387
(0.639) 		0.986
(1.00) 		0.00026
(0.00345) 		0.52
(0.754) 		0.885
(0.978) 		0.883
(0.978) 		0.752
(0.892) 		0.591
(0.806) 		0.965
(1.00) 		0.694
(0.844) 		0.323
(0.574) 		0.694
(0.844)
amp 7q36 3 320 (55%) 259 0.105
(0.294) 		0.178
(0.4) 		0.357
(0.615) 		0.989
(1.00) 		2e-05
(0.000432) 		0.457
(0.707) 		0.216
(0.459) 		0.115
(0.308) 		0.882
(0.978) 		0.654
(0.833) 		0.213
(0.454) 		0.503
(0.748) 		0.198
(0.434) 		0.264
(0.516)
amp 15q26 3 163 (28%) 416 0.085
(0.266) 		0.424
(0.672) 		0.508
(0.75) 		0.428
(0.675) 		1e-05
(0.000226) 		0.805
(0.927) 		0.968
(1.00) 		0.738
(0.877) 		0.313
(0.566) 		0.94
(1.00) 		0.154
(0.374) 		0.0664
(0.223) 		0.675
(0.833) 		0.786
(0.913)
del 1q41 97 (17%) 482 0.0896
(0.27) 		0.624
(0.82) 		0.3
(0.551) 		0.839
(0.949) 		1e-05
(0.000226) 		0.133
(0.338) 		0.395
(0.645) 		0.545
(0.771) 		0.609
(0.816) 		0.928
(0.996) 		0.92
(0.994) 		0.969
(1.00) 		0.455
(0.705)
del 2q22 1 137 (24%) 442 0.108
(0.297) 		0.271
(0.518) 		0.572
(0.798) 		0.0036
(0.0284) 		0.0746
(0.242) 		0.664
(0.833) 		0.964
(1.00) 		0.922
(0.994) 		0.466
(0.717) 		0.831
(0.943) 		0.479
(0.724) 		0.601
(0.812) 		1
(1.00) 		0.265
(0.516)
del 5q13 2 419 (72%) 160 0.746
(0.886) 		0.624
(0.82) 		0.898
(0.987) 		0.26
(0.512) 		1e-05
(0.000226) 		0.105
(0.294) 		0.502
(0.746) 		0.969
(1.00) 		0.323
(0.574) 		0.0903
(0.27) 		0.154
(0.374) 		0.107
(0.296) 		1
(1.00) 		0.724
(0.869)
del 7p22 1 253 (44%) 326 0.389
(0.641) 		0.515
(0.751) 		0.771
(0.908) 		0.0641
(0.217) 		1e-05
(0.000226) 		0.625
(0.82) 		0.923
(0.994) 		0.812
(0.931) 		0.298
(0.55) 		0.686
(0.84) 		0.348
(0.605) 		0.903
(0.987) 		0.231
(0.475) 		0.781
(0.911)
del 14q23 3 305 (53%) 274 0.065
(0.219) 		0.505
(0.749) 		0.654
(0.833) 		0.61
(0.816) 		3e-05
(0.000609) 		0.736
(0.877) 		0.657
(0.833) 		0.316
(0.57) 		0.265
(0.516) 		0.513
(0.75) 		0.898
(0.987) 		0.595
(0.806) 		0.666
(0.833) 		0.142
(0.359)
del 21q22 3 227 (39%) 352 0.37
(0.628) 		0.0406
(0.167) 		0.696
(0.844) 		0.205
(0.443) 		0.796
(0.92) 		0.264
(0.516) 		0.611
(0.816) 		0.593
(0.806) 		0.651
(0.833) 		0.486
(0.73) 		0.821
(0.938) 		0.728
(0.871) 		0.162
(0.382) 		0.929
(0.996)
del xp21 1 355 (61%) 224 0.404
(0.654) 		0.645
(0.832) 		0.0989
(0.285) 		0.8
(0.924) 		0.166
(0.385) 		0.0208
(0.106) 		0.681
(0.838) 		0.0563
(0.2) 		0.513
(0.75) 		0.474
(0.722) 		0.977
(1.00) 		0.716
(0.861) 		0.594
(0.806) 		0.282
(0.528)
amp 10q22 3 184 (32%) 395 0.369
(0.628) 		0.267
(0.517) 		0.608
(0.816) 		0.949
(1.00) 		0.0782
(0.251) 		0.845
(0.952) 		0.865
(0.969) 		0.841
(0.95) 		0.532
(0.763) 		0.571
(0.798) 		0.228
(0.474) 		0.647
(0.832) 		0.67
(0.833) 		0.302
(0.553)
del 2p25 3 120 (21%) 459 0.881
(0.978) 		0.27
(0.518) 		0.42
(0.67) 		0.156
(0.375) 		0.406
(0.657) 		0.636
(0.825) 		0.526
(0.76) 		0.831
(0.943) 		0.118
(0.314) 		0.662
(0.833) 		0.877
(0.978) 		0.951
(1.00) 		0.381
(0.633) 		0.425
(0.672)
del 10p15 3 120 (21%) 459 0.181
(0.404) 		0.71
(0.856) 		0.089
(0.269) 		0.321
(0.574) 		0.0964
(0.283) 		0.349
(0.605) 		0.329
(0.58) 		0.49
(0.735) 		0.829
(0.942) 		0.982
(1.00) 		0.254
(0.503) 		0.263
(0.516) 		0.594
(0.806) 		0.106
(0.295)
del 11q25 201 (35%) 378 0.625
(0.82) 		0.657
(0.833) 		0.208
(0.445) 		0.0519
(0.191) 		0.271
(0.518) 		0.418
(0.669) 		0.494
(0.738) 		0.39
(0.641) 		0.756
(0.896) 		0.158
(0.378) 		0.707
(0.854) 		0.27
(0.518) 		1
(1.00) 		0.772
(0.908)
del 17p12 491 (85%) 88 0.145
(0.363) 		0.335
(0.587) 		0.59
(0.806) 		0.691
(0.844) 		0.71
(0.856) 		0.323
(0.574) 		0.867
(0.969) 		0.661
(0.833) 		0.647
(0.832) 		0.463
(0.714) 		0.508
(0.75) 		0.209
(0.446) 		1
(1.00)
'amp_1p34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S1.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 1(1P34.3) MUTATED 58 114 120
AMP PEAK 1(1P34.3) WILD-TYPE 113 92 82

Figure S1.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S2.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 2(1Q21.3) MUTATED 86 114 167
AMP PEAK 2(1Q21.3) WILD-TYPE 85 92 35

Figure S2.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0021

Table S3.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 2(1Q21.3) MUTATED 128 92 141
AMP PEAK 2(1Q21.3) WILD-TYPE 44 83 80

Figure S3.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
AMP PEAK 2(1Q21.3) MUTATED 85 132 42
AMP PEAK 2(1Q21.3) WILD-TYPE 61 57 34

Figure S4.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.081

Table S5.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
AMP PEAK 2(1Q21.3) MUTATED 79 43 40 97
AMP PEAK 2(1Q21.3) WILD-TYPE 64 11 20 57

Figure S5.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00587 (Fisher's exact test), Q value = 0.041

Table S6.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 2(1Q21.3) MUTATED 54 42 119 68
AMP PEAK 2(1Q21.3) WILD-TYPE 51 29 46 38

Figure S6.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.2' versus 'MRNA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.12

Table S7.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 3(1Q42.2) MUTATED 133 106 66
AMP PEAK 3(1Q42.2) WILD-TYPE 82 110 60

Figure S7.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q42.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.13

Table S8.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 3(1Q42.2) MUTATED 174 74 57
AMP PEAK 3(1Q42.2) WILD-TYPE 136 84 32

Figure S8.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q42.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0082 (Fisher's exact test), Q value = 0.054

Table S9.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 3(1Q42.2) MUTATED 45 30 36 43 13 44 21 22 37 13
AMP PEAK 3(1Q42.2) WILD-TYPE 40 27 22 39 21 31 13 14 15 29

Figure S9.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_1q42.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S10.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 3(1Q42.2) MUTATED 88 87 147
AMP PEAK 3(1Q42.2) WILD-TYPE 83 119 55

Figure S10.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q42.2' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0011

Table S11.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 3(1Q42.2) MUTATED 119 87 108
AMP PEAK 3(1Q42.2) WILD-TYPE 53 88 113

Figure S11.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q42.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00287 (Fisher's exact test), Q value = 0.024

Table S12.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 3(1Q42.2) MUTATED 41 43 101 59
AMP PEAK 3(1Q42.2) WILD-TYPE 64 28 64 47

Figure S12.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_2p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.077

Table S13.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 4(2P23.2) MUTATED 123 67 51
AMP PEAK 4(2P23.2) WILD-TYPE 187 91 38

Figure S13.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S14.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 4(2P23.2) MUTATED 47 87 118
AMP PEAK 4(2P23.2) WILD-TYPE 124 119 84

Figure S14.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2p23.2' versus 'METHLYATION_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.034

Table S15.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 4(2P23.2) MUTATED 90 61 93
AMP PEAK 4(2P23.2) WILD-TYPE 82 114 128

Figure S15.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2p23.2' versus 'MRNASEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.14

Table S16.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 4(2P23.2) MUTATED 27 57 55
AMP PEAK 4(2P23.2) WILD-TYPE 52 51 58

Figure S16.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_2p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0066

Table S17.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 4(2P23.2) MUTATED 55 40 44
AMP PEAK 4(2P23.2) WILD-TYPE 91 19 51

Figure S17.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIR_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.14

Table S18.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
AMP PEAK 5(2Q31.2) MUTATED 73 61 117
AMP PEAK 5(2Q31.2) WILD-TYPE 86 103 115

Figure S18.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_2q31.2' versus 'MIR_CHIERARCHICAL'

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

Table S19.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 5(2Q31.2) MUTATED 30 20 32 42 14 36 18 15 31 13
AMP PEAK 5(2Q31.2) WILD-TYPE 55 37 26 40 20 39 16 21 21 29

Figure S19.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S20.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 5(2Q31.2) MUTATED 46 102 114
AMP PEAK 5(2Q31.2) WILD-TYPE 125 104 88

Figure S20.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 0.00765 (Fisher's exact test), Q value = 0.051

Table S21.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 5(2Q31.2) MUTATED 95 70 93
AMP PEAK 5(2Q31.2) WILD-TYPE 77 105 128

Figure S21.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'RPPA_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.13

Table S22.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
AMP PEAK 5(2Q31.2) MUTATED 64 96 25
AMP PEAK 5(2Q31.2) WILD-TYPE 82 93 51

Figure S22.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.058

Table S23.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 6(3Q26.2) MUTATED 167 191 108
AMP PEAK 6(3Q26.2) WILD-TYPE 48 25 18

Figure S23.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.12

Table S24.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 6(3Q26.2) MUTATED 257 141 68
AMP PEAK 6(3Q26.2) WILD-TYPE 53 17 21

Figure S24.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S25.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 6(3Q26.2) MUTATED 113 181 191
AMP PEAK 6(3Q26.2) WILD-TYPE 58 25 11

Figure S25.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.15

Table S26.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 6(3Q26.2) MUTATED 151 136 188
AMP PEAK 6(3Q26.2) WILD-TYPE 21 39 33

Figure S26.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MIR_CNMF'

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

Table S27.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
AMP PEAK 7(4P16.3) MUTATED 41 35 77
AMP PEAK 7(4P16.3) WILD-TYPE 118 129 155

Figure S27.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0051

Table S28.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 7(4P16.3) MUTATED 32 76 52
AMP PEAK 7(4P16.3) WILD-TYPE 139 130 150

Figure S28.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

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

Table S29.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 7(4P16.3) MUTATED 55 54 47
AMP PEAK 7(4P16.3) WILD-TYPE 117 121 174

Figure S29.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.096

Table S30.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 7(4P16.3) MUTATED 22 24 57 22
AMP PEAK 7(4P16.3) WILD-TYPE 83 47 108 84

Figure S30.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0034

Table S31.  Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 8(4Q13.3) MUTATED 17 54 42
AMP PEAK 8(4Q13.3) WILD-TYPE 154 152 160

Figure S31.  Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S32.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 9(5P15.33) MUTATED 60 123 126
AMP PEAK 9(5P15.33) WILD-TYPE 111 83 76

Figure S32.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.13

Table S33.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 9(5P15.33) MUTATED 91 26 47
AMP PEAK 9(5P15.33) WILD-TYPE 55 33 48

Figure S33.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.12

Table S34.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
AMP PEAK 9(5P15.33) MUTATED 61 115 72
AMP PEAK 9(5P15.33) WILD-TYPE 60 67 72

Figure S34.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_6p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.14

Table S35.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 10(6P22.3) MUTATED 167 71 55
AMP PEAK 10(6P22.3) WILD-TYPE 143 87 34

Figure S35.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S36.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 10(6P22.3) MUTATED 59 124 123
AMP PEAK 10(6P22.3) WILD-TYPE 112 82 79

Figure S36.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_6p22.3' versus 'METHLYATION_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.076

Table S37.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 10(6P22.3) MUTATED 104 78 117
AMP PEAK 10(6P22.3) WILD-TYPE 68 97 104

Figure S37.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q36.3' versus 'CN_CNMF'

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

Table S38.  Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 11(7Q36.3) MUTATED 69 124 127
AMP PEAK 11(7Q36.3) WILD-TYPE 102 82 75

Figure S38.  Get High-res Image Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S39.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 12(8P11.21) MUTATED 42 70 99
AMP PEAK 12(8P11.21) WILD-TYPE 129 136 103

Figure S39.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.089

Table S40.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 12(8P11.21) MUTATED 78 57 72
AMP PEAK 12(8P11.21) WILD-TYPE 94 118 149

Figure S40.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'RPPA_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.18

Table S41.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
AMP PEAK 12(8P11.21) MUTATED 41 77 29
AMP PEAK 12(8P11.21) WILD-TYPE 105 112 47

Figure S41.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S42.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 13(8Q24.21) MUTATED 144 188 110
AMP PEAK 13(8Q24.21) WILD-TYPE 71 28 16

Figure S42.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S43.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 13(8Q24.21) MUTATED 245 144 53
AMP PEAK 13(8Q24.21) WILD-TYPE 65 14 36

Figure S43.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'MIR_CHIERARCHICAL'

P value = 0.00283 (Fisher's exact test), Q value = 0.024

Table S44.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 13(8Q24.21) MUTATED 71 46 43 67 31 64 24 27 30 38
AMP PEAK 13(8Q24.21) WILD-TYPE 14 11 15 15 3 11 10 9 22 4

Figure S44.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S45.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 13(8Q24.21) MUTATED 113 200 148
AMP PEAK 13(8Q24.21) WILD-TYPE 58 6 54

Figure S45.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.034

Table S46.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 13(8Q24.21) MUTATED 124 137 189
AMP PEAK 13(8Q24.21) WILD-TYPE 48 38 32

Figure S46.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S47.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 13(8Q24.21) MUTATED 70 72 106
AMP PEAK 13(8Q24.21) WILD-TYPE 9 36 7

Figure S47.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S48.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 13(8Q24.21) MUTATED 120 38 90
AMP PEAK 13(8Q24.21) WILD-TYPE 26 21 5

Figure S48.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S49.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 14(10P15.3) MUTATED 45 81 126
AMP PEAK 14(10P15.3) WILD-TYPE 126 125 76

Figure S49.  Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_10p15.3' versus 'METHLYATION_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0073

Table S50.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 14(10P15.3) MUTATED 95 63 87
AMP PEAK 14(10P15.3) WILD-TYPE 77 112 134

Figure S50.  Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CNMF'

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

Table S51.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 14(10P15.3) MUTATED 25 55 45
AMP PEAK 14(10P15.3) WILD-TYPE 54 53 68

Figure S51.  Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNA_CNMF'

P value = 0.00521 (Fisher's exact test), Q value = 0.038

Table S52.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 16(11Q14.1) MUTATED 81 114 52
AMP PEAK 16(11Q14.1) WILD-TYPE 134 102 74

Figure S52.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00375 (Fisher's exact test), Q value = 0.029

Table S53.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 16(11Q14.1) MUTATED 154 66 27
AMP PEAK 16(11Q14.1) WILD-TYPE 156 92 62

Figure S53.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

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

Table S54.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 16(11Q14.1) MUTATED 54 117 86
AMP PEAK 16(11Q14.1) WILD-TYPE 117 89 116

Figure S54.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.023

Table S55.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 16(11Q14.1) MUTATED 82 59 111
AMP PEAK 16(11Q14.1) WILD-TYPE 90 116 110

Figure S55.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.098

Table S56.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 16(11Q14.1) MUTATED 75 18 47
AMP PEAK 16(11Q14.1) WILD-TYPE 71 41 48

Figure S56.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.17

Table S57.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 12 10
AMP PEAK 16(11Q14.1) MUTATED 8 2
AMP PEAK 16(11Q14.1) WILD-TYPE 4 8

Figure S57.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.12

Table S58.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 17(12P13.33) MUTATED 137 114 64
AMP PEAK 17(12P13.33) WILD-TYPE 78 102 62

Figure S58.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00309 (Fisher's exact test), Q value = 0.025

Table S59.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 17(12P13.33) MUTATED 175 77 63
AMP PEAK 17(12P13.33) WILD-TYPE 135 81 26

Figure S59.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S60.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 17(12P13.33) MUTATED 71 111 148
AMP PEAK 17(12P13.33) WILD-TYPE 100 95 54

Figure S60.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0028

Table S61.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 17(12P13.33) MUTATED 119 96 108
AMP PEAK 17(12P13.33) WILD-TYPE 53 79 113

Figure S61.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.098

Table S62.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 17(12P13.33) MUTATED 38 71 56
AMP PEAK 17(12P13.33) WILD-TYPE 41 37 57

Figure S62.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00778 (Fisher's exact test), Q value = 0.051

Table S63.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 17(12P13.33) MUTATED 45 45 103 57
AMP PEAK 17(12P13.33) WILD-TYPE 60 26 62 49

Figure S63.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIR_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.17

Table S64.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 18(12P12.1) MUTATED 41 27 31 47 20 37 21 17 39 17
AMP PEAK 18(12P12.1) WILD-TYPE 44 30 27 35 14 38 13 19 13 25

Figure S64.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S65.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 18(12P12.1) MUTATED 66 98 149
AMP PEAK 18(12P12.1) WILD-TYPE 105 108 53

Figure S65.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S66.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 18(12P12.1) MUTATED 117 87 102
AMP PEAK 18(12P12.1) WILD-TYPE 55 88 119

Figure S66.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.036

Table S67.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 18(12P12.1) MUTATED 32 70 63
AMP PEAK 18(12P12.1) WILD-TYPE 47 38 50

Figure S67.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00419 (Fisher's exact test), Q value = 0.032

Table S68.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 18(12P12.1) MUTATED 68 42 55
AMP PEAK 18(12P12.1) WILD-TYPE 78 17 40

Figure S68.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00532 (Fisher's exact test), Q value = 0.038

Table S69.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 18(12P12.1) MUTATED 43 44 100 52
AMP PEAK 18(12P12.1) WILD-TYPE 62 27 65 54

Figure S69.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.17

Table S70.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 2 2 6 4 2
AMP PEAK 18(12P12.1) MUTATED 4 0 0 2 4 2
AMP PEAK 18(12P12.1) WILD-TYPE 2 2 2 4 0 0

Figure S70.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'MRNA_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.023

Table S71.  Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 19(12Q15) MUTATED 99 65 47
AMP PEAK 19(12Q15) WILD-TYPE 116 151 79

Figure S71.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12q15' versus 'MIR_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.023

Table S72.  Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 19(12Q15) MUTATED 31 13 23 29 15 24 15 16 33 11
AMP PEAK 19(12Q15) WILD-TYPE 54 44 35 53 19 51 19 20 19 31

Figure S72.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S73.  Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 19(12Q15) MUTATED 52 58 112
AMP PEAK 19(12Q15) WILD-TYPE 119 148 90

Figure S73.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S74.  Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 19(12Q15) MUTATED 90 62 65
AMP PEAK 19(12Q15) WILD-TYPE 82 113 156

Figure S74.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.069

Table S75.  Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 19(12Q15) MUTATED 25 55 39
AMP PEAK 19(12Q15) WILD-TYPE 54 53 74

Figure S75.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.023

Table S76.  Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 19(12Q15) MUTATED 53 35 31
AMP PEAK 19(12Q15) WILD-TYPE 93 24 64

Figure S76.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'MRNA_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.091

Table S77.  Gene #20: 'amp_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 20(14Q11.2) MUTATED 70 48 26
AMP PEAK 20(14Q11.2) WILD-TYPE 145 168 100

Figure S77.  Get High-res Image Gene #20: 'amp_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00679 (Fisher's exact test), Q value = 0.046

Table S78.  Gene #20: 'amp_14q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 20(14Q11.2) MUTATED 26 16 15 21 10 8 10 11 21 5
AMP PEAK 20(14Q11.2) WILD-TYPE 59 41 43 61 24 67 24 25 31 37

Figure S78.  Get High-res Image Gene #20: 'amp_14q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_14q32.33' versus 'MIR_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.097

Table S79.  Gene #21: 'amp_14q32.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 21(14Q32.33) MUTATED 25 12 12 26 11 11 5 15 17 16
AMP PEAK 21(14Q32.33) WILD-TYPE 60 45 46 56 23 64 29 21 35 26

Figure S79.  Get High-res Image Gene #21: 'amp_14q32.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0022

Table S80.  Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 21(14Q32.33) MUTATED 41 77 38
AMP PEAK 21(14Q32.33) WILD-TYPE 130 129 164

Figure S80.  Get High-res Image Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S81.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 22(15Q26.3) MUTATED 34 90 39
AMP PEAK 22(15Q26.3) WILD-TYPE 137 116 163

Figure S81.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.031

Table S82.  Gene #23: 'amp_17q25.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 23(17Q25.3) MUTATED 53 95 67
AMP PEAK 23(17Q25.3) WILD-TYPE 118 111 135

Figure S82.  Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.078

Table S83.  Gene #23: 'amp_17q25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
AMP PEAK 23(17Q25.3) MUTATED 62 24 27 43
AMP PEAK 23(17Q25.3) WILD-TYPE 81 30 33 111

Figure S83.  Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.13

Table S84.  Gene #23: 'amp_17q25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 23(17Q25.3) MUTATED 36 31 49
AMP PEAK 23(17Q25.3) WILD-TYPE 43 77 64

Figure S84.  Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S85.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 24(18Q11.2) MUTATED 25 44 74
AMP PEAK 24(18Q11.2) WILD-TYPE 146 162 128

Figure S85.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.029

Table S86.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 24(18Q11.2) MUTATED 56 30 56
AMP PEAK 24(18Q11.2) WILD-TYPE 116 145 165

Figure S86.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0028

Table S87.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 25(19P13.12) MUTATED 136 115 51
AMP PEAK 25(19P13.12) WILD-TYPE 79 101 75

Figure S87.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0029

Table S88.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 25(19P13.12) MUTATED 186 64 52
AMP PEAK 25(19P13.12) WILD-TYPE 124 94 37

Figure S88.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'MIR_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.16

Table S89.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
AMP PEAK 25(19P13.12) MUTATED 85 77 139
AMP PEAK 25(19P13.12) WILD-TYPE 74 87 93

Figure S89.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_19p13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S90.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 25(19P13.12) MUTATED 72 92 151
AMP PEAK 25(19P13.12) WILD-TYPE 99 114 51

Figure S90.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S91.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 25(19P13.12) MUTATED 118 73 116
AMP PEAK 25(19P13.12) WILD-TYPE 54 102 105

Figure S91.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0013

Table S92.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
AMP PEAK 25(19P13.12) MUTATED 70 126 30
AMP PEAK 25(19P13.12) WILD-TYPE 76 63 46

Figure S92.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.015

Table S93.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
AMP PEAK 25(19P13.12) MUTATED 64 26 43 93
AMP PEAK 25(19P13.12) WILD-TYPE 79 28 17 61

Figure S93.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.17

Table S94.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 25(19P13.12) MUTATED 37 68 55
AMP PEAK 25(19P13.12) WILD-TYPE 42 40 58

Figure S94.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00656 (Fisher's exact test), Q value = 0.045

Table S95.  Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 26(19Q12) MUTATED 186 72 55
AMP PEAK 26(19Q12) WILD-TYPE 124 86 34

Figure S95.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'MIR_CNMF'

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

Table S96.  Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
AMP PEAK 26(19Q12) MUTATED 92 78 141
AMP PEAK 26(19Q12) WILD-TYPE 67 86 91

Figure S96.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S97.  Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 26(19Q12) MUTATED 67 83 172
AMP PEAK 26(19Q12) WILD-TYPE 104 123 30

Figure S97.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S98.  Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 26(19Q12) MUTATED 128 70 121
AMP PEAK 26(19Q12) WILD-TYPE 44 105 100

Figure S98.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.072

Table S99.  Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
AMP PEAK 26(19Q12) MUTATED 70 117 35
AMP PEAK 26(19Q12) WILD-TYPE 76 72 41

Figure S99.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S100.  Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 27(19Q13.2) MUTATED 51 71 123
AMP PEAK 27(19Q13.2) WILD-TYPE 120 135 79

Figure S100.  Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0014

Table S101.  Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 27(19Q13.2) MUTATED 94 56 91
AMP PEAK 27(19Q13.2) WILD-TYPE 78 119 130

Figure S101.  Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.13

Table S102.  Gene #27: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 27(19Q13.2) MUTATED 55 34 37
AMP PEAK 27(19Q13.2) WILD-TYPE 91 25 58

Figure S102.  Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 0.00538 (Fisher's exact test), Q value = 0.038

Table S103.  Gene #28: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 28(20P13) MUTATED 161 79 62
AMP PEAK 28(20P13) WILD-TYPE 149 79 27

Figure S103.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p13' versus 'MIR_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.14

Table S104.  Gene #28: 'amp_20p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 28(20P13) MUTATED 41 28 36 44 19 44 23 19 34 13
AMP PEAK 28(20P13) WILD-TYPE 44 29 22 38 15 31 11 17 18 29

Figure S104.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S105.  Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 28(20P13) MUTATED 69 97 151
AMP PEAK 28(20P13) WILD-TYPE 102 109 51

Figure S105.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S106.  Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 28(20P13) MUTATED 123 81 103
AMP PEAK 28(20P13) WILD-TYPE 49 94 118

Figure S106.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.087

Table S107.  Gene #28: 'amp_20p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 28(20P13) MUTATED 36 71 59
AMP PEAK 28(20P13) WILD-TYPE 43 37 54

Figure S107.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0448 (Fisher's exact test), Q value = 0.17

Table S108.  Gene #28: 'amp_20p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 28(20P13) MUTATED 74 41 51
AMP PEAK 28(20P13) WILD-TYPE 72 18 44

Figure S108.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0079

Table S109.  Gene #28: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 28(20P13) MUTATED 44 44 106 50
AMP PEAK 28(20P13) WILD-TYPE 61 27 59 56

Figure S109.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.023

Table S110.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 29(20Q11.21) MUTATED 144 110 78
AMP PEAK 29(20Q11.21) WILD-TYPE 71 106 48

Figure S110.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00308 (Fisher's exact test), Q value = 0.025

Table S111.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 29(20Q11.21) MUTATED 178 87 67
AMP PEAK 29(20Q11.21) WILD-TYPE 132 71 22

Figure S111.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'MIR_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.026

Table S112.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 29(20Q11.21) MUTATED 45 33 36 44 20 45 29 22 40 18
AMP PEAK 29(20Q11.21) WILD-TYPE 40 24 22 38 14 30 5 14 12 24

Figure S112.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S113.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 29(20Q11.21) MUTATED 79 95 174
AMP PEAK 29(20Q11.21) WILD-TYPE 92 111 28

Figure S113.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S114.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 29(20Q11.21) MUTATED 140 91 109
AMP PEAK 29(20Q11.21) WILD-TYPE 32 84 112

Figure S114.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.026

Table S115.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 29(20Q11.21) MUTATED 37 77 69
AMP PEAK 29(20Q11.21) WILD-TYPE 42 31 44

Figure S115.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00259 (Fisher's exact test), Q value = 0.023

Table S116.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 29(20Q11.21) MUTATED 80 47 56
AMP PEAK 29(20Q11.21) WILD-TYPE 66 12 39

Figure S116.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.008

Table S117.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 29(20Q11.21) MUTATED 52 46 119 57
AMP PEAK 29(20Q11.21) WILD-TYPE 53 25 46 49

Figure S117.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.066

Table S118.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 30(20Q13.33) MUTATED 164 136 86
AMP PEAK 30(20Q13.33) WILD-TYPE 51 80 40

Figure S118.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0083

Table S119.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 30(20Q13.33) MUTATED 207 103 76
AMP PEAK 30(20Q13.33) WILD-TYPE 103 55 13

Figure S119.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.33' versus 'MIR_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.014

Table S120.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 30(20Q13.33) MUTATED 49 35 41 52 29 54 29 26 45 25
AMP PEAK 30(20Q13.33) WILD-TYPE 36 22 17 30 5 21 5 10 7 17

Figure S120.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S121.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 30(20Q13.33) MUTATED 87 132 183
AMP PEAK 30(20Q13.33) WILD-TYPE 84 74 19

Figure S121.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S122.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 30(20Q13.33) MUTATED 144 109 140
AMP PEAK 30(20Q13.33) WILD-TYPE 28 66 81

Figure S122.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.12

Table S123.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
AMP PEAK 30(20Q13.33) MUTATED 49 86 78
AMP PEAK 30(20Q13.33) WILD-TYPE 30 22 35

Figure S123.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.023

Table S124.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 30(20Q13.33) MUTATED 95 52 66
AMP PEAK 30(20Q13.33) WILD-TYPE 51 7 29

Figure S124.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.18

Table S125.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 30(20Q13.33) MUTATED 69 53 128 68
AMP PEAK 30(20Q13.33) WILD-TYPE 36 18 37 38

Figure S125.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.084

Table S126.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 2 2 6 4 2
AMP PEAK 30(20Q13.33) MUTATED 6 2 0 3 4 2
AMP PEAK 30(20Q13.33) WILD-TYPE 0 0 2 3 0 0

Figure S126.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q12.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.14

Table S127.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 31(22Q12.2) MUTATED 11 7 15 16 4 16 5 8 3 2
AMP PEAK 31(22Q12.2) WILD-TYPE 74 50 43 66 30 59 29 28 49 40

Figure S127.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_22q12.2' versus 'CN_CNMF'

P value = 0.00762 (Fisher's exact test), Q value = 0.051

Table S128.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 31(22Q12.2) MUTATED 15 40 36
AMP PEAK 31(22Q12.2) WILD-TYPE 156 166 166

Figure S128.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_22q12.2' versus 'METHLYATION_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0088

Table S129.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 31(22Q12.2) MUTATED 27 14 48
AMP PEAK 31(22Q12.2) WILD-TYPE 145 161 173

Figure S129.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_22q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00154 (Fisher's exact test), Q value = 0.015

Table S130.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
AMP PEAK 31(22Q12.2) MUTATED 22 18 13 16
AMP PEAK 31(22Q12.2) WILD-TYPE 121 36 47 138

Figure S130.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.086

Table S131.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 31(22Q12.2) MUTATED 15 8 38 10
AMP PEAK 31(22Q12.2) WILD-TYPE 90 63 127 96

Figure S131.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S132.  Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 32(XP11.23) MUTATED 25 55 79
AMP PEAK 32(XP11.23) WILD-TYPE 146 151 123

Figure S132.  Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xp11.23' versus 'METHLYATION_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.018

Table S133.  Gene #32: 'amp_xp11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 32(XP11.23) MUTATED 64 37 53
AMP PEAK 32(XP11.23) WILD-TYPE 108 138 168

Figure S133.  Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.14

Table S134.  Gene #32: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 32(XP11.23) MUTATED 23 27 53 23
AMP PEAK 32(XP11.23) WILD-TYPE 82 44 112 83

Figure S134.  Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0046

Table S135.  Gene #33: 'amp_xq28' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 33(XQ28) MUTATED 46 96 78
AMP PEAK 33(XQ28) WILD-TYPE 125 110 124

Figure S135.  Get High-res Image Gene #33: 'amp_xq28' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.17

Table S136.  Gene #33: 'amp_xq28' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 12 10
AMP PEAK 33(XQ28) MUTATED 8 2
AMP PEAK 33(XQ28) WILD-TYPE 4 8

Figure S136.  Get High-res Image Gene #33: 'amp_xq28' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIR_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.13

Table S137.  Gene #34: 'del_1p36.11' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
DEL PEAK 1(1P36.11) MUTATED 74 92 99
DEL PEAK 1(1P36.11) WILD-TYPE 85 72 133

Figure S137.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #3: 'MIR_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00099

Table S138.  Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 1(1P36.11) MUTATED 87 113 69
DEL PEAK 1(1P36.11) WILD-TYPE 84 93 133

Figure S138.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.18

Table S139.  Gene #34: 'del_1p36.11' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 1(1P36.11) MUTATED 76 75 39
DEL PEAK 1(1P36.11) WILD-TYPE 70 114 37

Figure S139.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1q41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S140.  Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 2(1Q41) MUTATED 14 60 23
DEL PEAK 2(1Q41) WILD-TYPE 157 146 179

Figure S140.  Get High-res Image Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q22.1' versus 'MIR_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.028

Table S141.  Gene #37: 'del_2q22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 4(2Q22.1) MUTATED 22 8 8 20 14 18 4 17 12 10
DEL PEAK 4(2Q22.1) WILD-TYPE 63 49 50 62 20 57 30 19 40 32

Figure S141.  Get High-res Image Gene #37: 'del_2q22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.09

Table S142.  Gene #38: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 5(2Q37.3) MUTATED 51 78 41
DEL PEAK 5(2Q37.3) WILD-TYPE 164 138 85

Figure S142.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.13

Table S143.  Gene #38: 'del_2q37.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 5(2Q37.3) MUTATED 23 12 16 31 9 24 6 20 14 15
DEL PEAK 5(2Q37.3) WILD-TYPE 62 45 42 51 25 51 28 16 38 27

Figure S143.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S144.  Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 5(2Q37.3) MUTATED 35 86 54
DEL PEAK 5(2Q37.3) WILD-TYPE 136 120 148

Figure S144.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.12

Table S145.  Gene #38: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
DEL PEAK 5(2Q37.3) MUTATED 42 66 33
DEL PEAK 5(2Q37.3) WILD-TYPE 79 116 111

Figure S145.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.1

Table S146.  Gene #38: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 5(2Q37.3) MUTATED 45 19 52 25
DEL PEAK 5(2Q37.3) WILD-TYPE 60 52 113 81

Figure S146.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0074

Table S147.  Gene #39: 'del_3p26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 6(3P26.2) MUTATED 101 54 49
DEL PEAK 6(3P26.2) WILD-TYPE 209 104 40

Figure S147.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p26.2' versus 'MIR_CNMF'

P value = 0.00624 (Fisher's exact test), Q value = 0.043

Table S148.  Gene #39: 'del_3p26.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
DEL PEAK 6(3P26.2) MUTATED 54 47 102
DEL PEAK 6(3P26.2) WILD-TYPE 105 117 130

Figure S148.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_3p26.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00472 (Fisher's exact test), Q value = 0.035

Table S149.  Gene #39: 'del_3p26.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 6(3P26.2) MUTATED 29 20 12 34 13 26 17 16 28 8
DEL PEAK 6(3P26.2) WILD-TYPE 56 37 46 48 21 49 17 20 24 34

Figure S149.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S150.  Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 6(3P26.2) MUTATED 47 66 96
DEL PEAK 6(3P26.2) WILD-TYPE 124 140 106

Figure S150.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0071

Table S151.  Gene #39: 'del_3p26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 6(3P26.2) MUTATED 83 51 74
DEL PEAK 6(3P26.2) WILD-TYPE 89 124 147

Figure S151.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0091

Table S152.  Gene #39: 'del_3p26.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 6(3P26.2) MUTATED 16 46 50
DEL PEAK 6(3P26.2) WILD-TYPE 63 62 63

Figure S152.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0098

Table S153.  Gene #39: 'del_3p26.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 6(3P26.2) MUTATED 39 29 44
DEL PEAK 6(3P26.2) WILD-TYPE 107 30 51

Figure S153.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0368 (Fisher's exact test), Q value = 0.15

Table S154.  Gene #40: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 7(3Q13.31) MUTATED 27 7 14 15
DEL PEAK 7(3Q13.31) WILD-TYPE 116 47 46 139

Figure S154.  Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CNMF'

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

Table S155.  Gene #40: 'del_3q13.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 7(3Q13.31) MUTATED 5 16 21
DEL PEAK 7(3Q13.31) WILD-TYPE 74 92 92

Figure S155.  Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.12

Table S156.  Gene #41: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 8(4Q22.1) MUTATED 212 96 69
DEL PEAK 8(4Q22.1) WILD-TYPE 98 62 20

Figure S156.  Get High-res Image Gene #41: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.088

Table S157.  Gene #41: 'del_4q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 8(4Q22.1) MUTATED 114 128 152
DEL PEAK 8(4Q22.1) WILD-TYPE 57 78 50

Figure S157.  Get High-res Image Gene #41: 'del_4q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.008

Table S158.  Gene #42: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 9(4Q34.3) MUTATED 226 102 77
DEL PEAK 9(4Q34.3) WILD-TYPE 84 56 12

Figure S158.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.13

Table S159.  Gene #42: 'del_4q34.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 9(4Q34.3) MUTATED 66 42 41 65 22 49 29 24 43 23
DEL PEAK 9(4Q34.3) WILD-TYPE 19 15 17 17 12 26 5 12 9 19

Figure S159.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.13

Table S160.  Gene #42: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 9(4Q34.3) MUTATED 64 79 72
DEL PEAK 9(4Q34.3) WILD-TYPE 15 29 41

Figure S160.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.18

Table S161.  Gene #42: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 9(4Q34.3) MUTATED 110 46 59
DEL PEAK 9(4Q34.3) WILD-TYPE 36 13 36

Figure S161.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S162.  Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 10(5Q12.1) MUTATED 73 145 137
DEL PEAK 10(5Q12.1) WILD-TYPE 98 61 65

Figure S162.  Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0034

Table S163.  Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 10(5Q12.1) MUTATED 117 85 146
DEL PEAK 10(5Q12.1) WILD-TYPE 55 90 75

Figure S163.  Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S164.  Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 11(5Q13.2) MUTATED 92 180 147
DEL PEAK 11(5Q13.2) WILD-TYPE 79 26 55

Figure S164.  Get High-res Image Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S165.  Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 12(6Q27) MUTATED 121 162 97
DEL PEAK 12(6Q27) WILD-TYPE 50 44 105

Figure S165.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S166.  Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 12(6Q27) MUTATED 91 132 152
DEL PEAK 12(6Q27) WILD-TYPE 81 43 69

Figure S166.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0084

Table S167.  Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 12(6Q27) MUTATED 56 52 79
DEL PEAK 12(6Q27) WILD-TYPE 23 56 34

Figure S167.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.018

Table S168.  Gene #45: 'del_6q27' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 12(6Q27) MUTATED 92 26 69
DEL PEAK 12(6Q27) WILD-TYPE 54 33 26

Figure S168.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q27' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.12

Table S169.  Gene #45: 'del_6q27' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 12(6Q27) MUTATED 79 43 96 72
DEL PEAK 12(6Q27) WILD-TYPE 26 28 69 34

Figure S169.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S170.  Gene #46: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 13(7P22.1) MUTATED 48 135 70
DEL PEAK 13(7P22.1) WILD-TYPE 123 71 132

Figure S170.  Get High-res Image Gene #46: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p23.3' versus 'MRNA_CNMF'

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

Table S171.  Gene #47: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 14(8P23.3) MUTATED 132 157 85
DEL PEAK 14(8P23.3) WILD-TYPE 83 59 41

Figure S171.  Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.07

Table S172.  Gene #47: 'del_8p23.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 14(8P23.3) MUTATED 57 36 34 61 30 53 15 27 33 29
DEL PEAK 14(8P23.3) WILD-TYPE 28 21 24 21 4 22 19 9 19 13

Figure S172.  Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S173.  Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 14(8P23.3) MUTATED 78 162 148
DEL PEAK 14(8P23.3) WILD-TYPE 93 44 54

Figure S173.  Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p21.2' versus 'MRNA_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.17

Table S174.  Gene #48: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 15(8P21.2) MUTATED 138 160 94
DEL PEAK 15(8P21.2) WILD-TYPE 77 56 32

Figure S174.  Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p21.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00554 (Fisher's exact test), Q value = 0.039

Table S175.  Gene #48: 'del_8p21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 15(8P21.2) MUTATED 66 35 39 56 30 51 16 30 36 33
DEL PEAK 15(8P21.2) WILD-TYPE 19 22 19 26 4 24 18 6 16 9

Figure S175.  Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_8p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S176.  Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 15(8P21.2) MUTATED 88 166 152
DEL PEAK 15(8P21.2) WILD-TYPE 83 40 50

Figure S176.  Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p24.3' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0034

Table S177.  Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 16(9P24.3) MUTATED 109 73 66
DEL PEAK 16(9P24.3) WILD-TYPE 106 143 60

Figure S177.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S178.  Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 16(9P24.3) MUTATED 120 69 59
DEL PEAK 16(9P24.3) WILD-TYPE 190 89 30

Figure S178.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p24.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.08

Table S179.  Gene #49: 'del_9p24.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 16(9P24.3) MUTATED 34 21 28 30 18 27 16 16 36 20
DEL PEAK 16(9P24.3) WILD-TYPE 51 36 30 52 16 48 18 20 16 22

Figure S179.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_9p24.3' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00099

Table S180.  Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 16(9P24.3) MUTATED 92 90 75
DEL PEAK 16(9P24.3) WILD-TYPE 80 85 146

Figure S180.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9p24.3' versus 'MRNASEQ_CNMF'

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

Table S181.  Gene #49: 'del_9p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 16(9P24.3) MUTATED 26 57 53
DEL PEAK 16(9P24.3) WILD-TYPE 53 51 60

Figure S181.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_9q34.13' versus 'MRNA_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.094

Table S182.  Gene #50: 'del_9q34.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 17(9Q34.13) MUTATED 143 121 66
DEL PEAK 17(9Q34.13) WILD-TYPE 72 95 60

Figure S182.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.13' versus 'MRNA_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0089

Table S183.  Gene #50: 'del_9q34.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 17(9Q34.13) MUTATED 185 79 66
DEL PEAK 17(9Q34.13) WILD-TYPE 125 79 23

Figure S183.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S184.  Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 17(9Q34.13) MUTATED 93 98 151
DEL PEAK 17(9Q34.13) WILD-TYPE 78 108 51

Figure S184.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

'del_9q34.13' versus 'METHLYATION_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.094

Table S185.  Gene #50: 'del_9q34.13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 17(9Q34.13) MUTATED 115 91 132
DEL PEAK 17(9Q34.13) WILD-TYPE 57 84 89

Figure S185.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9q34.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.18

Table S186.  Gene #50: 'del_9q34.13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 17(9Q34.13) MUTATED 70 34 31 98
DEL PEAK 17(9Q34.13) WILD-TYPE 73 20 29 56

Figure S186.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_9q34.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00871 (Fisher's exact test), Q value = 0.056

Table S187.  Gene #50: 'del_9q34.13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 17(9Q34.13) MUTATED 82 46 54
DEL PEAK 17(9Q34.13) WILD-TYPE 64 13 41

Figure S187.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.13' versus 'MIRSEQ_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.18

Table S188.  Gene #50: 'del_9q34.13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
DEL PEAK 17(9Q34.13) MUTATED 65 107 98
DEL PEAK 17(9Q34.13) WILD-TYPE 56 75 46

Figure S188.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10q24.2' versus 'MRNA_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.025

Table S189.  Gene #52: 'del_10q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 19(10Q24.2) MUTATED 87 112 43
DEL PEAK 19(10Q24.2) WILD-TYPE 128 104 83

Figure S189.  Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q24.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00232 (Fisher's exact test), Q value = 0.022

Table S190.  Gene #52: 'del_10q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 19(10Q24.2) MUTATED 152 64 26
DEL PEAK 19(10Q24.2) WILD-TYPE 158 94 63

Figure S190.  Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q24.2' versus 'MIR_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.047

Table S191.  Gene #52: 'del_10q24.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
DEL PEAK 19(10Q24.2) MUTATED 70 56 116
DEL PEAK 19(10Q24.2) WILD-TYPE 89 108 116

Figure S191.  Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q24.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00086

Table S192.  Gene #52: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 19(10Q24.2) MUTATED 53 111 87
DEL PEAK 19(10Q24.2) WILD-TYPE 118 95 115

Figure S192.  Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q24.2' versus 'METHLYATION_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.019

Table S193.  Gene #52: 'del_10q24.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 19(10Q24.2) MUTATED 79 58 111
DEL PEAK 19(10Q24.2) WILD-TYPE 93 117 110

Figure S193.  Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q24.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.14

Table S194.  Gene #52: 'del_10q24.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 19(10Q24.2) MUTATED 52 32 27 71
DEL PEAK 19(10Q24.2) WILD-TYPE 91 22 33 83

Figure S194.  Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q24.2' versus 'MIRSEQ_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.016

Table S195.  Gene #52: 'del_10q24.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
DEL PEAK 19(10Q24.2) MUTATED 48 102 55
DEL PEAK 19(10Q24.2) WILD-TYPE 73 80 89

Figure S195.  Get High-res Image Gene #52: 'del_10q24.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S196.  Gene #53: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 20(11P15.5) MUTATED 77 163 106
DEL PEAK 20(11P15.5) WILD-TYPE 94 43 96

Figure S196.  Get High-res Image Gene #53: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00781 (Fisher's exact test), Q value = 0.051

Table S197.  Gene #53: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 20(11P15.5) MUTATED 89 100 148
DEL PEAK 20(11P15.5) WILD-TYPE 83 75 73

Figure S197.  Get High-res Image Gene #53: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00875 (Fisher's exact test), Q value = 0.056

Table S198.  Gene #53: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 20(11P15.5) MUTATED 76 38 91 56
DEL PEAK 20(11P15.5) WILD-TYPE 29 33 74 50

Figure S198.  Get High-res Image Gene #53: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MRNA_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.012

Table S199.  Gene #55: 'del_12q24.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 22(12Q24.33) MUTATED 62 99 51
DEL PEAK 22(12Q24.33) WILD-TYPE 153 117 75

Figure S199.  Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q24.33' versus 'MIR_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.083

Table S200.  Gene #55: 'del_12q24.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 22(12Q24.33) MUTATED 34 21 19 35 11 34 7 19 11 21
DEL PEAK 22(12Q24.33) WILD-TYPE 51 36 39 47 23 41 27 17 41 21

Figure S200.  Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S201.  Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 22(12Q24.33) MUTATED 56 113 51
DEL PEAK 22(12Q24.33) WILD-TYPE 115 93 151

Figure S201.  Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.1

Table S202.  Gene #55: 'del_12q24.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 22(12Q24.33) MUTATED 51 75 91
DEL PEAK 22(12Q24.33) WILD-TYPE 121 100 130

Figure S202.  Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.18

Table S203.  Gene #55: 'del_12q24.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 22(12Q24.33) MUTATED 33 29 45
DEL PEAK 22(12Q24.33) WILD-TYPE 46 79 68

Figure S203.  Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.12

Table S204.  Gene #55: 'del_12q24.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 22(12Q24.33) MUTATED 53 13 41
DEL PEAK 22(12Q24.33) WILD-TYPE 93 46 54

Figure S204.  Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.089

Table S205.  Gene #55: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
DEL PEAK 22(12Q24.33) MUTATED 42 82 43
DEL PEAK 22(12Q24.33) WILD-TYPE 79 100 101

Figure S205.  Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.005 (Fisher's exact test), Q value = 0.037

Table S206.  Gene #55: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 22(12Q24.33) MUTATED 54 20 60 33
DEL PEAK 22(12Q24.33) WILD-TYPE 51 51 105 73

Figure S206.  Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 0.00956 (Fisher's exact test), Q value = 0.061

Table S207.  Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 23(13Q14.2) MUTATED 133 150 67
DEL PEAK 23(13Q14.2) WILD-TYPE 82 66 59

Figure S207.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.09

Table S208.  Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 23(13Q14.2) MUTATED 211 88 51
DEL PEAK 23(13Q14.2) WILD-TYPE 99 70 38

Figure S208.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.17

Table S209.  Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 23(13Q14.2) MUTATED 52 37 42 52 26 37 16 27 32 29
DEL PEAK 23(13Q14.2) WILD-TYPE 33 20 16 30 8 38 18 9 20 13

Figure S209.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0033

Table S210.  Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 23(13Q14.2) MUTATED 90 150 124
DEL PEAK 23(13Q14.2) WILD-TYPE 81 56 78

Figure S210.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S211.  Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 23(13Q14.2) MUTATED 109 88 161
DEL PEAK 23(13Q14.2) WILD-TYPE 63 87 60

Figure S211.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.012

Table S212.  Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 23(13Q14.2) MUTATED 76 135 45
DEL PEAK 23(13Q14.2) WILD-TYPE 70 54 31

Figure S212.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00293 (Fisher's exact test), Q value = 0.024

Table S213.  Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 23(13Q14.2) MUTATED 73 32 42 109
DEL PEAK 23(13Q14.2) WILD-TYPE 70 22 18 45

Figure S213.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.1

Table S214.  Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 23(13Q14.2) MUTATED 54 77 61
DEL PEAK 23(13Q14.2) WILD-TYPE 25 31 52

Figure S214.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.17

Table S215.  Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 23(13Q14.2) MUTATED 101 40 51
DEL PEAK 23(13Q14.2) WILD-TYPE 45 19 44

Figure S215.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S216.  Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 24(14Q23.3) MUTATED 70 104 131
DEL PEAK 24(14Q23.3) WILD-TYPE 101 102 71

Figure S216.  Get High-res Image Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'MRNA_CNMF'

P value = 0.00613 (Fisher's exact test), Q value = 0.043

Table S217.  Gene #58: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 25(15Q11.2) MUTATED 130 98 62
DEL PEAK 25(15Q11.2) WILD-TYPE 85 118 64

Figure S217.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.15

Table S218.  Gene #58: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 25(15Q11.2) MUTATED 164 71 55
DEL PEAK 25(15Q11.2) WILD-TYPE 146 87 34

Figure S218.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q11.2' versus 'MIR_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.067

Table S219.  Gene #58: 'del_15q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
DEL PEAK 25(15Q11.2) MUTATED 77 74 138
DEL PEAK 25(15Q11.2) WILD-TYPE 82 90 94

Figure S219.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_15q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00593 (Fisher's exact test), Q value = 0.042

Table S220.  Gene #58: 'del_15q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 25(15Q11.2) MUTATED 35 28 36 40 19 43 23 21 32 12
DEL PEAK 25(15Q11.2) WILD-TYPE 50 29 22 42 15 32 11 15 20 30

Figure S220.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S221.  Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 25(15Q11.2) MUTATED 68 76 155
DEL PEAK 25(15Q11.2) WILD-TYPE 103 130 47

Figure S221.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S222.  Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 25(15Q11.2) MUTATED 114 82 100
DEL PEAK 25(15Q11.2) WILD-TYPE 58 93 121

Figure S222.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0065

Table S223.  Gene #58: 'del_15q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 25(15Q11.2) MUTATED 29 70 54
DEL PEAK 25(15Q11.2) WILD-TYPE 50 38 59

Figure S223.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.12

Table S224.  Gene #58: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
DEL PEAK 25(15Q11.2) MUTATED 54 110 79
DEL PEAK 25(15Q11.2) WILD-TYPE 67 72 65

Figure S224.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00956 (Fisher's exact test), Q value = 0.061

Table S225.  Gene #58: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 25(15Q11.2) MUTATED 43 40 102 58
DEL PEAK 25(15Q11.2) WILD-TYPE 62 31 63 48

Figure S225.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MRNA_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.12

Table S226.  Gene #59: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 26(15Q15.1) MUTATED 150 124 78
DEL PEAK 26(15Q15.1) WILD-TYPE 65 92 48

Figure S226.  Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.1' versus 'MIR_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.11

Table S227.  Gene #59: 'del_15q15.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
DEL PEAK 26(15Q15.1) MUTATED 95 94 162
DEL PEAK 26(15Q15.1) WILD-TYPE 64 70 70

Figure S227.  Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_15q15.1' versus 'MIR_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.023

Table S228.  Gene #59: 'del_15q15.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 26(15Q15.1) MUTATED 43 32 42 51 23 52 23 26 41 18
DEL PEAK 26(15Q15.1) WILD-TYPE 42 25 16 31 11 23 11 10 11 24

Figure S228.  Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S229.  Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 26(15Q15.1) MUTATED 81 115 167
DEL PEAK 26(15Q15.1) WILD-TYPE 90 91 35

Figure S229.  Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S230.  Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 26(15Q15.1) MUTATED 134 97 129
DEL PEAK 26(15Q15.1) WILD-TYPE 38 78 92

Figure S230.  Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.09

Table S231.  Gene #59: 'del_15q15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 26(15Q15.1) MUTATED 42 79 70
DEL PEAK 26(15Q15.1) WILD-TYPE 37 29 43

Figure S231.  Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S232.  Gene #59: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 26(15Q15.1) MUTATED 58 48 124 61
DEL PEAK 26(15Q15.1) WILD-TYPE 47 23 41 45

Figure S232.  Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.13

Table S233.  Gene #60: 'del_16p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 27(16P13.3) MUTATED 42 29 25 45 21 43 21 29 25 19
DEL PEAK 27(16P13.3) WILD-TYPE 43 28 33 37 13 32 13 7 27 23

Figure S233.  Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.17

Table S234.  Gene #60: 'del_16p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 27(16P13.3) MUTATED 85 104 31
DEL PEAK 27(16P13.3) WILD-TYPE 61 85 45

Figure S234.  Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_16q22.1' versus 'MIR_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.14

Table S235.  Gene #61: 'del_16q22.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
DEL PEAK 28(16Q22.1) MUTATED 127 120 195
DEL PEAK 28(16Q22.1) WILD-TYPE 32 44 37

Figure S235.  Get High-res Image Gene #61: 'del_16q22.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_16q22.1' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0075

Table S236.  Gene #61: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 28(16Q22.1) MUTATED 119 171 171
DEL PEAK 28(16Q22.1) WILD-TYPE 52 35 31

Figure S236.  Get High-res Image Gene #61: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.18

Table S237.  Gene #61: 'del_16q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 28(16Q22.1) MUTATED 89 50 140 83
DEL PEAK 28(16Q22.1) WILD-TYPE 16 21 25 23

Figure S237.  Get High-res Image Gene #61: 'del_16q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0022

Table S238.  Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 29(16Q23.1) MUTATED 114 168 170
DEL PEAK 29(16Q23.1) WILD-TYPE 57 38 32

Figure S238.  Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0497 (Fisher's exact test), Q value = 0.18

Table S239.  Gene #62: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 29(16Q23.1) MUTATED 87 51 140 79
DEL PEAK 29(16Q23.1) WILD-TYPE 18 20 25 27

Figure S239.  Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0075

Table S240.  Gene #64: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 31(17Q11.2) MUTATED 136 184 152
DEL PEAK 31(17Q11.2) WILD-TYPE 35 22 50

Figure S240.  Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.025

Table S241.  Gene #64: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 31(17Q11.2) MUTATED 127 145 193
DEL PEAK 31(17Q11.2) WILD-TYPE 45 30 28

Figure S241.  Get High-res Image Gene #64: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_18q23' versus 'CN_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.023

Table S242.  Gene #65: 'del_18q23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 32(18Q23) MUTATED 103 154 124
DEL PEAK 32(18Q23) WILD-TYPE 68 52 78

Figure S242.  Get High-res Image Gene #65: 'del_18q23' versus Molecular Subtype #5: 'CN_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.18

Table S243.  Gene #65: 'del_18q23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 32(18Q23) MUTATED 86 45 65
DEL PEAK 32(18Q23) WILD-TYPE 60 14 30

Figure S243.  Get High-res Image Gene #65: 'del_18q23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0046

Table S244.  Gene #66: 'del_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 33(19P13.3) MUTATED 142 178 192
DEL PEAK 33(19P13.3) WILD-TYPE 29 28 10

Figure S244.  Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.095

Table S245.  Gene #66: 'del_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 33(19P13.3) MUTATED 161 153 187
DEL PEAK 33(19P13.3) WILD-TYPE 11 22 34

Figure S245.  Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.0041 (Fisher's exact test), Q value = 0.031

Table S246.  Gene #66: 'del_19p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 33(19P13.3) MUTATED 129 175 59
DEL PEAK 33(19P13.3) WILD-TYPE 17 14 17

Figure S246.  Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_19q13.33' versus 'MRNA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0028

Table S247.  Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 34(19Q13.33) MUTATED 127 117 46
DEL PEAK 34(19Q13.33) WILD-TYPE 88 99 80

Figure S247.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00223 (Fisher's exact test), Q value = 0.021

Table S248.  Gene #67: 'del_19q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 34(19Q13.33) MUTATED 178 64 48
DEL PEAK 34(19Q13.33) WILD-TYPE 132 94 41

Figure S248.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.33' versus 'MIR_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.18

Table S249.  Gene #67: 'del_19q13.33' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
DEL PEAK 34(19Q13.33) MUTATED 78 76 135
DEL PEAK 34(19Q13.33) WILD-TYPE 81 88 97

Figure S249.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #3: 'MIR_CNMF'

'del_19q13.33' versus 'MIR_CHIERARCHICAL'

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

Table S250.  Gene #67: 'del_19q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 34(19Q13.33) MUTATED 44 35 36 50 10 32 18 16 23 25
DEL PEAK 34(19Q13.33) WILD-TYPE 41 22 22 32 24 43 16 20 29 17

Figure S250.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.083

Table S251.  Gene #67: 'del_19q13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 34(19Q13.33) MUTATED 86 93 120
DEL PEAK 34(19Q13.33) WILD-TYPE 85 113 82

Figure S251.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.022

Table S252.  Gene #67: 'del_19q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 34(19Q13.33) MUTATED 103 73 118
DEL PEAK 34(19Q13.33) WILD-TYPE 69 102 103

Figure S252.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.14

Table S253.  Gene #67: 'del_19q13.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 34(19Q13.33) MUTATED 59 33 35 74
DEL PEAK 34(19Q13.33) WILD-TYPE 84 21 25 80

Figure S253.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.088

Table S254.  Gene #67: 'del_19q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
DEL PEAK 34(19Q13.33) MUTATED 38 63 44
DEL PEAK 34(19Q13.33) WILD-TYPE 41 45 69

Figure S254.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.09

Table S255.  Gene #67: 'del_19q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 34(19Q13.33) MUTATED 71 37 37
DEL PEAK 34(19Q13.33) WILD-TYPE 75 22 58

Figure S255.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.09

Table S256.  Gene #68: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 35(19Q13.43) MUTATED 121 104 51
DEL PEAK 35(19Q13.43) WILD-TYPE 94 112 75

Figure S256.  Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0017

Table S257.  Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 35(19Q13.43) MUTATED 84 80 121
DEL PEAK 35(19Q13.43) WILD-TYPE 87 126 81

Figure S257.  Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S258.  Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 35(19Q13.43) MUTATED 105 64 111
DEL PEAK 35(19Q13.43) WILD-TYPE 67 111 110

Figure S258.  Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.17

Table S259.  Gene #68: 'del_19q13.43' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 12 10
DEL PEAK 35(19Q13.43) MUTATED 8 2
DEL PEAK 35(19Q13.43) WILD-TYPE 4 8

Figure S259.  Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.11

Table S260.  Gene #68: 'del_19q13.43' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 2 2 6 4 2
DEL PEAK 35(19Q13.43) MUTATED 3 2 2 1 0 2
DEL PEAK 35(19Q13.43) WILD-TYPE 3 0 0 5 4 0

Figure S260.  Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0406 (Fisher's exact test), Q value = 0.17

Table S261.  Gene #69: 'del_21q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 36(21Q22.3) MUTATED 117 58 46
DEL PEAK 36(21Q22.3) WILD-TYPE 193 100 43

Figure S261.  Get High-res Image Gene #69: 'del_21q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'MIR_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.14

Table S262.  Gene #70: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
DEL PEAK 37(22Q13.32) MUTATED 136 135 211
DEL PEAK 37(22Q13.32) WILD-TYPE 23 29 21

Figure S262.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.094

Table S263.  Gene #70: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 37(22Q13.32) MUTATED 138 182 183
DEL PEAK 37(22Q13.32) WILD-TYPE 33 24 19

Figure S263.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.16

Table S264.  Gene #70: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 37(22Q13.32) MUTATED 124 171 60
DEL PEAK 37(22Q13.32) WILD-TYPE 22 18 16

Figure S264.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.17

Table S265.  Gene #70: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 37(22Q13.32) MUTATED 115 46 53 141
DEL PEAK 37(22Q13.32) WILD-TYPE 28 8 7 13

Figure S265.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.15

Table S266.  Gene #70: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
DEL PEAK 37(22Q13.32) MUTATED 97 164 128
DEL PEAK 37(22Q13.32) WILD-TYPE 24 18 16

Figure S266.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.11

Table S267.  Gene #71: 'del_xp21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 38(XP21.1) MUTATED 93 107 150
DEL PEAK 38(XP21.1) WILD-TYPE 79 68 71

Figure S267.  Get High-res Image Gene #71: 'del_xp21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

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/OV-TP/19783383/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/20141012/OV-TP.transferedmergedcluster.txt

  • Number of patients = 579

  • Number of significantly focal cnvs = 71

  • Number of molecular subtypes = 14

  • 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.

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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