Correlation between copy number variations of arm-level result and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1R210TQ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1R210TQ
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 14 molecular subtypes across 579 patients, 273 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

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

  • 2p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • 5p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 7p gain cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

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

  • 8p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

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

  • 9p gain cnv correlated to 'MRNA_CNMF',  'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 13q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 16p gain cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'MIR_CNMF' and 'MIR_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • 18p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • xp gain cnv correlated to 'CN_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'MIR_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'MRNA_CNMF'.

  • 7q loss cnv correlated to 'MRNA_CNMF'.

  • 8p loss cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 9q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 11p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 12p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_CNMF'.

  • 13q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • 15q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 17q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • 18p loss cnv correlated to 'MIR_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'MIR_CHIERARCHICAL',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 20q loss cnv correlated to 'MIR_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 22q loss cnv correlated to 'MRNA_CNMF',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • xp loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 273 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
2p gain 187 (32%) 392 1e-05
(0.000261) 		1e-05
(0.000261) 		0.162
(0.428) 		0.00056
(0.00765) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.00421
(0.0366) 		0.427
(0.72) 		2e-05
(0.000469) 		1e-05
(0.000261) 		0.518
(0.8) 		0.0222
(0.124) 		0.276
(0.577) 		0.372
(0.67)
15q loss 281 (49%) 298 0.00069
(0.0089) 		0.0162
(0.0992) 		0.00038
(0.00559) 		0.00017
(0.00291) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.149
(0.409) 		0.918
(1.00) 		0.0145
(0.0942) 		0.289
(0.592) 		0.0155
(0.098) 		0.0009
(0.0109) 		0.493
(0.78) 		0.0522
(0.215)
2q gain 154 (27%) 425 0.0002
(0.00333) 		6e-05
(0.00121) 		0.547
(0.824) 		0.00418
(0.0366) 		1e-05
(0.000261) 		0.00021
(0.00344) 		0.0833
(0.285) 		0.896
(0.997) 		4e-05
(0.00085) 		0.00025
(0.00393) 		0.377
(0.673) 		0.0074
(0.0566) 		0.684
(0.908) 		0.732
(0.918)
12p gain 257 (44%) 322 2e-05
(0.000469) 		0.0026
(0.026) 		0.637
(0.883) 		0.00119
(0.0134) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.0963
(0.314) 		0.665
(0.896) 		0.00025
(0.00393) 		0.00098
(0.0115) 		0.188
(0.472) 		0.00024
(0.00388) 		0.275
(0.577) 		0.375
(0.672)
20p gain 287 (50%) 292 1e-05
(0.000261) 		0.00089
(0.0109) 		0.0838
(0.285) 		0.00014
(0.00255) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.487
(0.774) 		0.245
(0.54) 		0.0108
(0.0737) 		0.0411
(0.184) 		0.876
(0.985) 		0.00666
(0.052) 		0.939
(1.00) 		0.245
(0.54)
20q gain 326 (56%) 253 1e-05
(0.000261) 		0.00069
(0.0089) 		0.19
(0.474) 		0.00013
(0.00245) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.503
(0.789) 		0.05
(0.21) 		0.0717
(0.262) 		0.00874
(0.0635) 		0.789
(0.94) 		0.00781
(0.0582) 		0.717
(0.914) 		0.16
(0.426)
5q loss 228 (39%) 351 0.00032
(0.0049) 		0.00177
(0.019) 		0.265
(0.566) 		0.0126
(0.0839) 		3e-05
(0.000662) 		1e-05
(0.000261) 		0.146
(0.408) 		0.519
(0.801) 		0.0011
(0.0126) 		0.00254
(0.0258) 		0.717
(0.914) 		0.00397
(0.0356) 		0.587
(0.856) 		0.962
(1.00)
9q loss 287 (50%) 292 0.0347
(0.164) 		0.00738
(0.0566) 		0.159
(0.426) 		0.0262
(0.137) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.658
(0.893) 		0.572
(0.844) 		0.00354
(0.0323) 		0.00145
(0.0159) 		0.598
(0.861) 		0.0313
(0.153) 		0.203
(0.495) 		0.575
(0.847)
12q gain 178 (31%) 401 0.00566
(0.0458) 		0.0713
(0.261) 		0.986
(1.00) 		0.141
(0.401) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.0509
(0.212) 		0.448
(0.737) 		0.0295
(0.148) 		0.0436
(0.191) 		0.14
(0.4) 		0.0087
(0.0635) 		0.0353
(0.165) 		0.376
(0.673)
3p loss 97 (17%) 482 1e-05
(0.000261) 		0.00066
(0.00871) 		0.671
(0.899) 		0.00074
(0.00923) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.109
(0.339) 		0.0379
(0.173) 		0.0956
(0.313) 		0.00135
(0.0149) 		0.107
(0.336) 		0.0756
(0.27) 		0.237
(0.531) 		0.726
(0.915)
8q loss 91 (16%) 488 0.0291
(0.146) 		0.00269
(0.0262) 		0.479
(0.771) 		0.213
(0.509) 		0.00263
(0.026) 		0.00265
(0.026) 		0.2
(0.491) 		0.327
(0.627) 		0.00946
(0.0679) 		0.00273
(0.0263) 		0.69
(0.911) 		0.0135
(0.0891) 		1
(1.00) 		0.291
(0.594)
22q loss 431 (74%) 148 0.00055
(0.00761) 		0.103
(0.326) 		0.0102
(0.0715) 		0.202
(0.495) 		1e-05
(0.000261) 		8e-05
(0.00156) 		0.0104
(0.0716) 		0.0432
(0.19) 		0.137
(0.393) 		0.0173
(0.103) 		0.0828
(0.284) 		0.647
(0.889) 		0.607
(0.869) 		0.38
(0.673)
1q gain 223 (39%) 356 0.148
(0.409) 		0.122
(0.364) 		0.272
(0.574) 		0.055
(0.22) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.429
(0.72) 		0.552
(0.826) 		0.0175
(0.103) 		0.0323
(0.156) 		0.577
(0.848) 		0.0209
(0.118) 		0.0182
(0.106) 		0.16
(0.426)
6p gain 172 (30%) 407 2e-05
(0.000469) 		0.0056
(0.0456) 		0.53
(0.81) 		0.0182
(0.106) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.792
(0.94) 		0.738
(0.922) 		0.165
(0.431) 		0.00073
(0.00921) 		0.707
(0.914) 		0.0652
(0.247) 		0.456
(0.744) 		0.667
(0.897)
6q gain 100 (17%) 479 8e-05
(0.00156) 		0.129
(0.373) 		0.334
(0.635) 		0.0121
(0.0817) 		2e-05
(0.000469) 		2e-05
(0.000469) 		0.864
(0.984) 		0.686
(0.908) 		0.11
(0.339) 		0.0537
(0.218) 		0.765
(0.936) 		0.0152
(0.0973) 		0.0157
(0.098) 		0.197
(0.485)
10p gain 189 (33%) 390 0.00027
(0.00419) 		0.0208
(0.118) 		0.711
(0.914) 		0.399
(0.691) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.867
(0.984) 		0.918
(1.00) 		0.00186
(0.0196) 		0.112
(0.342) 		0.453
(0.741) 		0.00043
(0.00617) 		0.791
(0.94) 		0.876
(0.985)
10q gain 109 (19%) 470 0.00516
(0.0423) 		0.0289
(0.146) 		0.048
(0.205) 		0.295
(0.598) 		0.00755
(0.0574) 		1e-05
(0.000261) 		0.798
(0.945) 		0.368
(0.665) 		0.0173
(0.103) 		0.124
(0.366) 		0.631
(0.882) 		0.191
(0.475) 		0.555
(0.829) 		0.871
(0.984)
13q gain 61 (11%) 518 0.00294
(0.0281) 		0.00018
(0.00304) 		0.235
(0.531) 		0.0164
(0.0994) 		4e-05
(0.00085) 		0.00061
(0.00814) 		0.32
(0.62) 		0.817
(0.958) 		0.0341
(0.163) 		0.115
(0.348) 		0.433
(0.721) 		0.0719
(0.262)
3q loss 42 (7%) 537 0.00812
(0.0601) 		0.0688
(0.255) 		0.238
(0.533) 		0.00993
(0.0704) 		0.0172
(0.103) 		0.00037
(0.00552) 		0.263
(0.564) 		0.126
(0.369) 		0.0548
(0.22) 		0.034
(0.163) 		0.101
(0.322) 		0.00095
(0.0112) 		0.259
(0.56) 		0.638
(0.883)
5p loss 134 (23%) 445 0.0885
(0.297) 		0.0453
(0.196) 		1
(1.00) 		0.0813
(0.283) 		0.00073
(0.00921) 		0.0123
(0.0823) 		0.0995
(0.32) 		0.316
(0.615) 		0.00165
(0.0179) 		0.00343
(0.0316) 		0.98
(1.00) 		0.0499
(0.21)
12p loss 79 (14%) 500 0.00707
(0.0548) 		0.0115
(0.0784) 		0.31
(0.61) 		0.0101
(0.0714) 		1e-05
(0.000261) 		0.281
(0.584) 		0.636
(0.882) 		0.544
(0.821) 		0.429
(0.72) 		0.161
(0.427) 		0.00046
(0.00652) 		0.00613
(0.0485) 		0.527
(0.809) 		0.406
(0.696)
13q loss 308 (53%) 271 0.101
(0.322) 		0.00431
(0.0372) 		0.622
(0.88) 		0.019
(0.109) 		0.00344
(0.0316) 		0.00182
(0.0193) 		0.0258
(0.136) 		0.0275
(0.141) 		0.083
(0.284) 		0.218
(0.512) 		0.0798
(0.278) 		0.569
(0.842) 		0.791
(0.94) 		0.72
(0.915)
11p loss 200 (35%) 379 0.0254
(0.134) 		0.00925
(0.0668) 		0.83
(0.965) 		0.0853
(0.288) 		0.00504
(0.0416) 		0.00321
(0.0301) 		0.327
(0.627) 		0.816
(0.958) 		0.111
(0.34) 		0.0967
(0.314) 		0.0309
(0.152) 		0.187
(0.471) 		0.056
(0.223) 		0.486
(0.774)
8q gain 249 (43%) 330 0.211
(0.508) 		0.00263
(0.026) 		0.557
(0.829) 		0.476
(0.769) 		0.0495
(0.21) 		0.0608
(0.237) 		0.605
(0.867) 		0.504
(0.789) 		0.00482
(0.0404) 		0.0401
(0.182) 		0.255
(0.559) 		0.987
(1.00) 		0.672
(0.899) 		0.531
(0.81)
9p gain 91 (16%) 488 0.0236
(0.129) 		0.439
(0.726) 		0.0274
(0.141) 		0.88
(0.985) 		1e-05
(0.000261) 		0.0127
(0.0845) 		0.635
(0.882) 		0.63
(0.882) 		0.731
(0.918) 		0.714
(0.914) 		0.103
(0.326) 		0.164
(0.43) 		0.356
(0.656) 		0.378
(0.673)
16q gain 32 (6%) 547 0.0163
(0.0994) 		0.0261
(0.137) 		0.416
(0.709) 		0.131
(0.379) 		0.404
(0.695) 		0.209
(0.508) 		0.927
(1.00) 		0.171
(0.444) 		0.0662
(0.249) 		0.341
(0.642) 		0.0297
(0.148) 		0.035
(0.164)
9p loss 264 (46%) 315 0.00115
(0.0131) 		0.0036
(0.0325) 		0.232
(0.528) 		0.133
(0.383) 		0.038
(0.173) 		0.00081
(0.01) 		0.881
(0.985) 		0.225
(0.517) 		0.179
(0.457) 		0.09
(0.301) 		0.0888
(0.297) 		0.229
(0.524) 		0.748
(0.931) 		0.0913
(0.304)
14q loss 217 (37%) 362 0.169
(0.44) 		0.215
(0.51) 		0.874
(0.985) 		0.327
(0.627) 		1e-05
(0.000261) 		0.00231
(0.0237) 		0.762
(0.936) 		0.714
(0.914) 		0.0042
(0.0366) 		1e-05
(0.000261) 		0.648
(0.889) 		0.295
(0.598) 		0.531
(0.81) 		0.53
(0.81)
16q loss 413 (71%) 166 0.112
(0.343) 		0.902
(0.999) 		0.00865
(0.0635) 		0.0951
(0.312) 		3e-05
(0.000662) 		0.00041
(0.00596) 		0.302
(0.605) 		0.496
(0.783) 		0.173
(0.445) 		0.716
(0.914) 		0.0249
(0.134) 		0.0846
(0.287) 		0.693
(0.913) 		0.832
(0.965)
19p loss 184 (32%) 395 0.797
(0.945) 		0.431
(0.721) 		0.806
(0.951) 		0.0438
(0.191) 		0.0526
(0.215) 		0.0755
(0.27) 		0.0291
(0.146) 		0.0299
(0.149) 		1
(1.00) 		0.143
(0.403) 		0.823
(0.96) 		0.259
(0.56) 		0.0379
(0.173) 		0.142
(0.401)
1p gain 173 (30%) 406 0.0413
(0.184) 		0.586
(0.856) 		0.181
(0.46) 		0.778
(0.94) 		1e-05
(0.000261) 		0.00049
(0.00686) 		0.485
(0.774) 		0.764
(0.936) 		0.283
(0.586) 		0.523
(0.804) 		0.5
(0.785) 		0.385
(0.679) 		0.108
(0.336) 		0.128
(0.373)
7p gain 177 (31%) 402 0.383
(0.678) 		0.595
(0.861) 		0.0236
(0.129) 		0.158
(0.426) 		1e-05
(0.000261) 		1e-05
(0.000261) 		0.836
(0.966) 		0.173
(0.445) 		0.907
(1.00) 		0.577
(0.848) 		0.337
(0.637) 		0.148
(0.409) 		0.71
(0.914) 		0.961
(1.00)
7q gain 203 (35%) 376 0.586
(0.856) 		0.0471
(0.203) 		0.0743
(0.267) 		0.334
(0.635) 		1e-05
(0.000261) 		5e-05
(0.00102) 		0.7
(0.914) 		0.322
(0.622) 		0.864
(0.984) 		0.971
(1.00) 		0.301
(0.603) 		0.662
(0.894) 		0.924
(1.00) 		0.872
(0.985)
18p gain 119 (21%) 460 0.106
(0.334) 		0.11
(0.339) 		0.664
(0.895) 		0.541
(0.819) 		0.00106
(0.0123) 		1e-05
(0.000261) 		0.054
(0.218) 		0.911
(1.00) 		0.0372
(0.172) 		0.714
(0.914) 		0.66
(0.894) 		0.177
(0.454) 		1
(1.00) 		1
(1.00)
21q gain 107 (18%) 472 0.451
(0.74) 		0.9
(0.998) 		0.766
(0.936) 		0.534
(0.81) 		0.00059
(0.00797) 		0.00194
(0.0202) 		0.101
(0.322) 		0.365
(0.663) 		0.192
(0.475) 		0.147
(0.408) 		0.0147
(0.0951) 		0.0505
(0.211)
10q loss 127 (22%) 452 0.222
(0.515) 		0.828
(0.964) 		0.00586
(0.047) 		0.47
(0.763) 		3e-05
(0.000662) 		0.0419
(0.186) 		0.717
(0.914) 		0.627
(0.882) 		0.724
(0.915) 		0.771
(0.937) 		0.366
(0.664) 		0.36
(0.661) 		0.217
(0.512) 		0.64
(0.884)
11q loss 147 (25%) 432 0.199
(0.489) 		1
(1.00) 		0.252
(0.554) 		0.38
(0.673) 		0.00093
(0.0111) 		0.00436
(0.0374) 		0.267
(0.568) 		0.401
(0.691) 		0.124
(0.366) 		0.254
(0.557) 		0.016
(0.0987) 		0.16
(0.426) 		0.237
(0.531) 		0.727
(0.917)
12q loss 107 (18%) 472 0.237
(0.531) 		0.0632
(0.244) 		0.556
(0.829) 		0.392
(0.687) 		0.0104
(0.0716) 		0.129
(0.373) 		0.0372
(0.172) 		0.515
(0.799) 		0.163
(0.428) 		0.0513
(0.213) 		0.0156
(0.098) 		0.0635
(0.244) 		0.354
(0.655) 		0.0849
(0.287)
16p loss 335 (58%) 244 0.0734
(0.266) 		0.714
(0.914) 		0.0819
(0.284) 		0.436
(0.724) 		0.0236
(0.129) 		0.0269
(0.14) 		0.0762
(0.27) 		0.969
(1.00) 		0.148
(0.409) 		0.777
(0.94) 		0.0787
(0.276) 		0.0273
(0.141) 		1
(1.00) 		0.713
(0.914)
17q loss 387 (67%) 192 0.158
(0.426) 		0.017
(0.102) 		0.157
(0.425) 		0.0177
(0.103) 		0.644
(0.887) 		0.293
(0.596) 		0.712
(0.914) 		0.291
(0.594) 		0.0046
(0.0388) 		0.0657
(0.248) 		0.103
(0.326) 		0.639
(0.884) 		1
(1.00) 		0.879
(0.985)
xp loss 328 (57%) 251 0.116
(0.349) 		0.315
(0.615) 		0.671
(0.899) 		0.678
(0.902) 		0.06
(0.235) 		0.00767
(0.0579) 		0.418
(0.709) 		0.0139
(0.0911) 		0.712
(0.914) 		0.988
(1.00) 		0.0253
(0.134) 		0.597
(0.861) 		0.428
(0.72) 		0.944
(1.00)
xq loss 285 (49%) 294 0.405
(0.696) 		0.532
(0.81) 		0.77
(0.936) 		0.953
(1.00) 		0.0145
(0.0942) 		0.00135
(0.0149) 		0.287
(0.59) 		0.0428
(0.189) 		0.648
(0.889) 		0.704
(0.914) 		0.126
(0.37) 		0.76
(0.936) 		0.867
(0.984) 		0.924
(1.00)
3p gain 162 (28%) 417 0.914
(1.00) 		0.708
(0.914) 		0.221
(0.515) 		0.62
(0.88) 		0.00322
(0.0301) 		0.0402
(0.182) 		0.777
(0.94) 		0.629
(0.882) 		0.335
(0.635) 		0.943
(1.00) 		0.345
(0.646) 		0.688
(0.91) 		0.868
(0.984) 		0.712
(0.914)
3q gain 278 (48%) 301 0.0537
(0.218) 		0.853
(0.977) 		0.315
(0.615) 		0.285
(0.587) 		1e-05
(0.000261) 		0.00015
(0.00265) 		0.949
(1.00) 		0.173
(0.445) 		0.237
(0.531) 		0.533
(0.81) 		0.365
(0.663) 		0.0574
(0.227) 		1
(1.00) 		0.372
(0.67)
4p gain 61 (11%) 518 0.269
(0.571) 		0.298
(0.6) 		0.0795
(0.278) 		0.0927
(0.307) 		0.172
(0.445) 		0.025
(0.134) 		0.346
(0.646) 		0.304
(0.605) 		0.635
(0.882) 		0.285
(0.587) 		0.612
(0.874) 		0.0195
(0.111) 		0.766
(0.936) 		1
(1.00)
4q gain 32 (6%) 547 0.787
(0.94) 		0.764
(0.936) 		0.0647
(0.246) 		0.297
(0.6) 		0.0351
(0.164) 		0.035
(0.164) 		0.635
(0.882) 		0.052
(0.215) 		0.661
(0.894) 		0.401
(0.691) 		0.684
(0.908) 		0.0597
(0.235)
5p gain 199 (34%) 380 0.567
(0.84) 		0.677
(0.902) 		0.722
(0.915) 		0.761
(0.936) 		0.00014
(0.00255) 		0.00405
(0.036) 		0.364
(0.663) 		0.378
(0.673) 		0.379
(0.673) 		0.378
(0.673) 		0.363
(0.663) 		0.712
(0.914) 		0.755
(0.936) 		0.393
(0.687)
8p gain 125 (22%) 454 0.224
(0.517) 		0.0278
(0.142) 		0.973
(1.00) 		0.285
(0.587) 		0.141
(0.401) 		0.97
(1.00) 		0.304
(0.605) 		0.363
(0.663) 		0.265
(0.566) 		0.0737
(0.266) 		0.0236
(0.129) 		0.696
(0.914)
11p gain 73 (13%) 506 0.964
(1.00) 		0.138
(0.396) 		0.782
(0.94) 		0.605
(0.867) 		0.0487
(0.207) 		0.0685
(0.255) 		0.00963
(0.0687) 		0.161
(0.426) 		0.515
(0.799) 		0.349
(0.649) 		0.734
(0.918) 		0.865
(0.984)
11q gain 114 (20%) 465 0.385
(0.679) 		0.211
(0.508) 		0.73
(0.918) 		0.357
(0.657) 		0.00015
(0.00265) 		0.00311
(0.0295) 		0.397
(0.691) 		0.434
(0.722) 		0.579
(0.85) 		0.269
(0.571) 		0.832
(0.965) 		0.835
(0.966) 		0.219
(0.514) 		0.58
(0.851)
16p gain 59 (10%) 520 0.023
(0.127) 		0.00502
(0.0416) 		0.485
(0.774) 		0.222
(0.515) 		0.113
(0.344) 		0.301
(0.603) 		0.661
(0.894) 		0.147
(0.408) 		0.185
(0.467) 		0.861
(0.983) 		0.0966
(0.314) 		0.062
(0.24)
17p gain 21 (4%) 558 0.149
(0.409) 		0.0785
(0.276) 		0.0412
(0.184) 		0.037
(0.172) 		0.153
(0.418) 		0.367
(0.665) 		0.149
(0.409) 		0.592
(0.861) 		0.509
(0.794) 		0.124
(0.366) 		0.295
(0.598) 		0.748
(0.931)
17q gain 41 (7%) 538 0.016
(0.0987) 		0.00655
(0.0515) 		0.216
(0.51) 		0.0573
(0.227) 		0.731
(0.918) 		0.243
(0.539) 		0.505
(0.789) 		0.699
(0.914) 		0.928
(1.00) 		0.146
(0.408) 		0.789
(0.94) 		0.933
(1.00)
18q gain 67 (12%) 512 0.781
(0.94) 		0.351
(0.651) 		0.205
(0.497) 		0.441
(0.729) 		0.0152
(0.0973) 		0.0103
(0.0715) 		1
(1.00) 		0.785
(0.94) 		0.515
(0.799) 		0.785
(0.94) 		0.149
(0.409) 		0.092
(0.305) 		1
(1.00) 		1
(1.00)
19p gain 170 (29%) 409 0.424
(0.715) 		0.482
(0.774) 		0.658
(0.893) 		0.33
(0.629) 		1e-05
(0.000261) 		0.00593
(0.0473) 		0.472
(0.764) 		0.759
(0.936) 		0.29
(0.594) 		0.142
(0.401) 		0.708
(0.914) 		0.347
(0.647) 		1
(1.00) 		0.731
(0.918)
19q gain 163 (28%) 416 0.432
(0.721) 		0.768
(0.936) 		0.954
(1.00) 		0.18
(0.458) 		1e-05
(0.000261) 		0.00204
(0.0211) 		0.725
(0.915) 		0.533
(0.81) 		0.109
(0.339) 		0.122
(0.364) 		0.741
(0.925) 		0.62
(0.88) 		0.878
(0.985) 		0.945
(1.00)
4p loss 315 (54%) 264 0.397
(0.691) 		0.0475
(0.204) 		0.226
(0.517) 		0.55
(0.826) 		0.00017
(0.00291) 		0.311
(0.61) 		0.182
(0.463) 		0.834
(0.966) 		0.655
(0.893) 		0.847
(0.972) 		0.186
(0.467) 		0.116
(0.349) 		0.25
(0.55) 		0.314
(0.615)
6q loss 240 (41%) 339 0.336
(0.636) 		0.143
(0.402) 		0.421
(0.713) 		0.0343
(0.163) 		0.437
(0.725) 		0.0637
(0.244) 		0.523
(0.804) 		0.838
(0.966) 		0.0984
(0.317) 		0.0168
(0.101) 		0.899
(0.998) 		0.618
(0.879) 		0.12
(0.36) 		0.489
(0.776)
8p loss 272 (47%) 307 0.63
(0.882) 		0.76
(0.936) 		0.185
(0.467) 		0.839
(0.966) 		0.101
(0.322) 		0.00443
(0.0377) 		0.0981
(0.317) 		0.358
(0.657) 		0.958
(1.00) 		0.713
(0.914) 		0.809
(0.953) 		0.033
(0.159) 		0.566
(0.84) 		0.858
(0.981)
18p loss 233 (40%) 346 0.48
(0.771) 		0.889
(0.991) 		0.274
(0.576) 		0.025
(0.134) 		0.398
(0.691) 		0.0745
(0.267) 		0.212
(0.509) 		0.437
(0.725) 		0.714
(0.914) 		0.047
(0.203) 		0.701
(0.914) 		0.594
(0.861) 		0.565
(0.839) 		0.49
(0.778)
19q loss 175 (30%) 404 0.671
(0.899) 		0.355
(0.656) 		0.839
(0.966) 		0.0156
(0.098) 		0.00778
(0.0582) 		0.212
(0.509) 		0.0609
(0.237) 		0.0944
(0.311) 		0.829
(0.964) 		0.55
(0.826) 		0.784
(0.94) 		0.161
(0.426) 		0.214
(0.509) 		0.0549
(0.22)
21q loss 202 (35%) 377 0.955
(1.00) 		0.0702
(0.258) 		0.432
(0.721) 		0.189
(0.474) 		0.0321
(0.156) 		0.0312
(0.153) 		0.497
(0.783) 		0.769
(0.936) 		0.87
(0.984) 		0.511
(0.796) 		0.0686
(0.255) 		0.656
(0.893) 		0.634
(0.882) 		0.43
(0.721)
9q gain 43 (7%) 536 0.401
(0.691) 		0.168
(0.438) 		0.0524
(0.215) 		0.675
(0.901) 		0.0249
(0.134) 		0.788
(0.94) 		0.914
(1.00) 		0.261
(0.562) 		0.242
(0.539) 		0.307
(0.608) 		0.346
(0.646) 		0.628
(0.882)
xp gain 78 (13%) 501 0.955
(1.00) 		0.635
(0.882) 		0.975
(1.00) 		0.594
(0.861) 		0.0412
(0.184) 		0.602
(0.865) 		0.767
(0.936) 		0.317
(0.616) 		0.909
(1.00) 		0.975
(1.00) 		0.258
(0.56) 		0.0644
(0.246)
xq gain 108 (19%) 471 0.821
(0.96) 		1
(1.00) 		0.792
(0.94) 		0.164
(0.43) 		0.00011
(0.0021) 		0.307
(0.608) 		0.217
(0.512) 		0.0878
(0.296) 		0.966
(1.00) 		0.822
(0.96) 		0.849
(0.974) 		0.484
(0.774) 		0.879
(0.985) 		0.557
(0.829)
1p loss 61 (11%) 518 0.298
(0.6) 		0.00034
(0.00514) 		0.329
(0.629) 		0.201
(0.493) 		0.523
(0.804) 		0.218
(0.512) 		0.215
(0.51) 		0.645
(0.888) 		0.706
(0.914) 		0.308
(0.609) 		0.193
(0.478) 		0.515
(0.799)
2p loss 52 (9%) 527 0.442
(0.729) 		0.0301
(0.149) 		0.774
(0.939) 		0.449
(0.739) 		0.787
(0.94) 		0.595
(0.861) 		0.718
(0.914) 		0.936
(1.00) 		0.455
(0.744) 		0.901
(0.998) 		0.829
(0.964) 		0.304
(0.605)
4q loss 363 (63%) 216 0.213
(0.509) 		0.106
(0.333) 		0.314
(0.615) 		0.642
(0.886) 		5e-05
(0.00102) 		0.399
(0.691) 		0.213
(0.509) 		0.259
(0.56) 		0.867
(0.984) 		0.346
(0.646) 		0.272
(0.573) 		0.124
(0.366) 		0.16
(0.426) 		0.122
(0.364)
7p loss 122 (21%) 457 0.0208
(0.118) 		0.593
(0.861) 		0.413
(0.707) 		0.733
(0.918) 		0.387
(0.682) 		0.615
(0.876) 		0.518
(0.8) 		0.9
(0.998) 		0.0825
(0.284) 		0.234
(0.531) 		0.963
(1.00) 		0.885
(0.988) 		1
(1.00) 		0.726
(0.915)
7q loss 79 (14%) 500 0.0227
(0.127) 		0.121
(0.364) 		0.787
(0.94) 		0.256
(0.559) 		0.604
(0.867) 		0.686
(0.908) 		0.785
(0.94) 		0.369
(0.666) 		0.335
(0.635) 		0.0502
(0.21) 		0.718
(0.914) 		0.894
(0.996) 		1
(1.00) 		0.871
(0.984)
18q loss 288 (50%) 291 0.263
(0.564) 		0.813
(0.956) 		0.632
(0.882) 		0.96
(1.00) 		0.5
(0.785) 		0.613
(0.874) 		0.815
(0.958) 		0.222
(0.515) 		0.417
(0.709) 		0.0185
(0.107) 		0.821
(0.96) 		0.657
(0.893) 		0.275
(0.577) 		0.416
(0.709)
20q loss 33 (6%) 546 0.494
(0.781) 		0.668
(0.899) 		0.0445
(0.194) 		0.535
(0.811) 		0.563
(0.837) 		0.633
(0.882) 		0.0683
(0.255) 		0.271
(0.572) 		0.228
(0.522) 		0.421
(0.713) 		0.393
(0.687) 		0.401
(0.691)
5q gain 59 (10%) 520 0.261
(0.562) 		0.283
(0.586) 		0.858
(0.981) 		0.836
(0.966) 		0.323
(0.622) 		0.635
(0.882) 		0.842
(0.967) 		0.926
(1.00) 		0.499
(0.785) 		0.373
(0.67) 		0.19
(0.474) 		0.867
(0.984)
14q gain 58 (10%) 521 0.807
(0.951) 		0.154
(0.42) 		0.234
(0.53) 		0.75
(0.931) 		0.781
(0.94) 		0.258
(0.56) 		0.769
(0.936) 		0.69
(0.911) 		0.915
(1.00) 		0.881
(0.985) 		0.278
(0.58) 		0.747
(0.931)
15q gain 38 (7%) 541 0.881
(0.985) 		0.622
(0.88) 		0.129
(0.373) 		0.683
(0.908) 		0.31
(0.61) 		0.798
(0.945) 		0.658
(0.893) 		0.0941
(0.31) 		0.596
(0.861) 		0.392
(0.687) 		0.403
(0.693) 		0.32
(0.62)
22q gain 23 (4%) 556 0.0724
(0.263) 		0.586
(0.856) 		0.363
(0.663) 		0.508
(0.793) 		0.706
(0.914) 		0.342
(0.643) 		0.462
(0.751) 		0.225
(0.517) 		0.0764
(0.27) 		0.0828
(0.284) 		0.477
(0.77) 		0.122
(0.364) 		1
(1.00) 		0.634
(0.882)
1q loss 40 (7%) 539 0.221
(0.515) 		0.0638
(0.244) 		0.226
(0.517) 		0.613
(0.874) 		0.955
(1.00) 		0.222
(0.515) 		0.909
(1.00) 		0.913
(1.00) 		0.904
(1) 		0.761
(0.936) 		0.323
(0.622) 		0.884
(0.987)
2q loss 62 (11%) 517 0.53
(0.81) 		0.551
(0.826) 		0.8
(0.945) 		0.163
(0.428) 		0.7
(0.914) 		0.572
(0.844) 		0.841
(0.967) 		0.299
(0.601) 		0.456
(0.744) 		1
(1.00) 		0.997
(1.00) 		0.151
(0.413) 		1
(1.00) 		0.0763
(0.27)
6p loss 161 (28%) 418 0.155
(0.422) 		0.0695
(0.256) 		0.24
(0.535) 		0.343
(0.644) 		0.354
(0.655) 		0.27
(0.572) 		0.391
(0.687) 		0.651
(0.891) 		0.459
(0.747) 		0.0672
(0.252) 		0.306
(0.607) 		0.0597
(0.235) 		0.257
(0.56) 		0.765
(0.936)
10p loss 99 (17%) 480 0.111
(0.34) 		0.963
(1.00) 		0.236
(0.531) 		0.467
(0.758) 		0.478
(0.771) 		0.655
(0.893) 		0.985
(1.00) 		0.726
(0.915) 		0.551
(0.826) 		0.822
(0.96) 		0.243
(0.539) 		0.802
(0.947) 		0.764
(0.936) 		0.767
(0.936)
17p loss 478 (83%) 101 0.672
(0.899) 		0.328
(0.627) 		0.276
(0.577) 		0.211
(0.508) 		0.451
(0.74) 		0.486
(0.774) 		0.485
(0.774) 		0.653
(0.893) 		0.129
(0.373) 		0.23
(0.525) 		0.587
(0.856) 		0.348
(0.648)
20p loss 51 (9%) 528 0.974
(1.00) 		0.778
(0.94) 		0.717
(0.914) 		0.723
(0.915) 		0.263
(0.564) 		0.184
(0.467) 		0.196
(0.483) 		0.32
(0.62) 		0.415
(0.709) 		0.284
(0.587) 		0.422
(0.713) 		0.543
(0.821)
'1p gain' versus 'MRNA_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.18

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
1P GAIN MUTATED 50 33 25 56
1P GAIN WILD-TYPE 126 79 93 95

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
1P GAIN MUTATED 103 25 45
1P GAIN WILD-TYPE 139 105 162

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0069

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
1P GAIN MUTATED 39 33 35 63
1P GAIN WILD-TYPE 74 65 152 107

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
1Q GAIN MUTATED 133 37 53
1Q GAIN WILD-TYPE 109 93 154

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
1Q GAIN MUTATED 43 49 43 84
1Q GAIN WILD-TYPE 70 49 144 86

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.1

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
1Q GAIN MUTATED 27 56 39
1Q GAIN WILD-TYPE 52 53 73

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.16

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
1Q GAIN MUTATED 54 33 35
1Q GAIN WILD-TYPE 92 26 60

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.12

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
1Q GAIN MUTATED 29 30 72 49
1Q GAIN WILD-TYPE 76 41 93 57

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.11

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 6 5 5
1Q GAIN MUTATED 5 2 0 4
1Q GAIN WILD-TYPE 1 4 5 1

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
2P GAIN MUTATED 87 31 24 33
2P GAIN WILD-TYPE 89 81 94 118

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
2P GAIN MUTATED 77 48 50
2P GAIN WILD-TYPE 233 110 39

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0077

Table S12.  Gene #3: '2p gain' 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
2P GAIN MUTATED 21 16 22 22 10 21 17 7 30 9
2P GAIN WILD-TYPE 64 41 36 60 24 54 17 29 22 33

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
2P GAIN MUTATED 117 22 48
2P GAIN WILD-TYPE 125 108 159

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
2P GAIN MUTATED 35 39 31 75
2P GAIN WILD-TYPE 78 59 156 95

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 0.00421 (Fisher's exact test), Q value = 0.037

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
2P GAIN MUTATED 47 74 14
2P GAIN WILD-TYPE 99 115 62

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00047

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
2P GAIN MUTATED 13 55 40
2P GAIN WILD-TYPE 66 54 72

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
2P GAIN MUTATED 34 38 36
2P GAIN WILD-TYPE 112 21 59

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.12

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
2P GAIN MUTATED 23 27 64 33
2P GAIN WILD-TYPE 82 44 101 73

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0033

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
2Q GAIN MUTATED 68 25 25 28
2Q GAIN WILD-TYPE 108 87 93 123

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
2Q GAIN MUTATED 69 36 41
2Q GAIN WILD-TYPE 241 122 48

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00418 (Fisher's exact test), Q value = 0.037

Table S21.  Gene #4: '2q gain' 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
2Q GAIN MUTATED 16 13 17 18 9 20 15 4 24 9
2Q GAIN WILD-TYPE 69 44 41 64 25 55 19 32 28 33

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
2Q GAIN MUTATED 100 14 40
2Q GAIN WILD-TYPE 142 116 167

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0034

Table S23.  Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
2Q GAIN MUTATED 32 30 29 59
2Q GAIN WILD-TYPE 81 68 158 111

Figure S23.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00085

Table S24.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
2Q GAIN MUTATED 9 44 31
2Q GAIN WILD-TYPE 70 65 81

Figure S24.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0039

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
2Q GAIN MUTATED 29 29 26
2Q GAIN WILD-TYPE 117 30 69

Figure S25.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0074 (Fisher's exact test), Q value = 0.057

Table S26.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
2Q GAIN MUTATED 16 22 55 29
2Q GAIN WILD-TYPE 89 49 110 77

Figure S26.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.03

Table S27.  Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
3P GAIN MUTATED 82 23 57
3P GAIN WILD-TYPE 160 107 150

Figure S27.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.18

Table S28.  Gene #5: '3p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
3P GAIN MUTATED 41 27 40 51
3P GAIN WILD-TYPE 72 71 147 119

Figure S28.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S29.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
3Q GAIN MUTATED 149 37 92
3Q GAIN WILD-TYPE 93 93 115

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0026

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
3Q GAIN MUTATED 61 53 64 92
3Q GAIN WILD-TYPE 52 45 123 78

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.13

Table S31.  Gene #7: '4p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
4P GAIN MUTATED 11 14 10 23
4P GAIN WILD-TYPE 102 84 177 147

Figure S31.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.11

Table S32.  Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
4P GAIN MUTATED 7 12 26 7
4P GAIN WILD-TYPE 98 59 139 99

Figure S32.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.16

Table S33.  Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
4Q GAIN MUTATED 14 2 16
4Q GAIN WILD-TYPE 228 128 191

Figure S33.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.16

Table S34.  Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
4Q GAIN MUTATED 4 6 5 16
4Q GAIN WILD-TYPE 109 92 182 154

Figure S34.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0026

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
5P GAIN MUTATED 95 25 79
5P GAIN WILD-TYPE 147 105 128

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.036

Table S36.  Gene #9: '5p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
5P GAIN MUTATED 52 31 49 63
5P GAIN WILD-TYPE 61 67 138 107

Figure S36.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00047

Table S37.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
6P GAIN MUTATED 68 37 13 46
6P GAIN WILD-TYPE 108 75 105 105

Figure S37.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0056 (Fisher's exact test), Q value = 0.046

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
6P GAIN MUTATED 80 45 39
6P GAIN WILD-TYPE 230 113 50

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.11

Table S39.  Gene #11: '6p gain' 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
6P GAIN MUTATED 21 15 14 19 12 28 11 12 25 6
6P GAIN WILD-TYPE 64 42 44 63 22 47 23 24 27 36

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S40.  Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
6P GAIN MUTATED 96 15 61
6P GAIN WILD-TYPE 146 115 146

Figure S40.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S41.  Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
6P GAIN MUTATED 43 31 29 65
6P GAIN WILD-TYPE 70 67 158 105

Figure S41.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0092

Table S42.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
6P GAIN MUTATED 36 31 31
6P GAIN WILD-TYPE 110 28 64

Figure S42.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0016

Table S43.  Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
6Q GAIN MUTATED 40 23 5 28
6Q GAIN WILD-TYPE 136 89 113 123

Figure S43.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.082

Table S44.  Gene #12: '6q gain' 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
6Q GAIN MUTATED 12 5 9 14 8 9 10 8 17 3
6Q GAIN WILD-TYPE 73 52 49 68 26 66 24 28 35 39

Figure S44.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00047

Table S45.  Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
6Q GAIN MUTATED 60 7 33
6Q GAIN WILD-TYPE 182 123 174

Figure S45.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00047

Table S46.  Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
6Q GAIN MUTATED 30 14 14 41
6Q GAIN WILD-TYPE 83 84 173 129

Figure S46.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.097

Table S47.  Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
6Q GAIN MUTATED 15 20 36 12
6Q GAIN WILD-TYPE 90 51 129 94

Figure S47.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.098

Table S48.  Gene #12: '6q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 6 5 5
6Q GAIN MUTATED 1 0 3 4
6Q GAIN WILD-TYPE 5 6 2 1

Figure S48.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIR_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.13

Table S49.  Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
7P GAIN MUTATED 52 30 88
7P GAIN WILD-TYPE 129 101 155

Figure S49.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S50.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
7P GAIN MUTATED 105 29 43
7P GAIN WILD-TYPE 137 101 164

Figure S50.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S51.  Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
7P GAIN MUTATED 42 30 31 71
7P GAIN WILD-TYPE 71 68 156 99

Figure S51.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.2

Table S52.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
7Q GAIN MUTATED 120 43 31
7Q GAIN WILD-TYPE 190 115 58

Figure S52.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S53.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
7Q GAIN MUTATED 113 29 61
7Q GAIN WILD-TYPE 129 101 146

Figure S53.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

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

Table S54.  Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
7Q GAIN MUTATED 46 32 42 78
7Q GAIN WILD-TYPE 67 66 145 92

Figure S54.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.14

Table S55.  Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
8P GAIN MUTATED 55 43 24
8P GAIN WILD-TYPE 255 115 65

Figure S55.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.13

Table S56.  Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
8P GAIN MUTATED 22 36 27 14
8P GAIN WILD-TYPE 49 99 114 86

Figure S56.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00263 (Fisher's exact test), Q value = 0.026

Table S57.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
8Q GAIN MUTATED 121 87 34
8Q GAIN WILD-TYPE 189 71 55

Figure S57.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.21

Table S58.  Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
8Q GAIN MUTATED 108 44 97
8Q GAIN WILD-TYPE 134 86 110

Figure S58.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.04

Table S59.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
8Q GAIN MUTATED 43 37 59
8Q GAIN WILD-TYPE 36 72 53

Figure S59.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0401 (Fisher's exact test), Q value = 0.18

Table S60.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
8Q GAIN MUTATED 67 20 52
8Q GAIN WILD-TYPE 79 39 43

Figure S60.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.13

Table S61.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
9P GAIN MUTATED 28 14 12 35
9P GAIN WILD-TYPE 148 98 106 116

Figure S61.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MIR_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.14

Table S62.  Gene #17: '9p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
9P GAIN MUTATED 36 12 41
9P GAIN WILD-TYPE 145 119 202

Figure S62.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S63.  Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
9P GAIN MUTATED 55 6 30
9P GAIN WILD-TYPE 187 124 177

Figure S63.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.085

Table S64.  Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
9P GAIN MUTATED 21 8 24 37
9P GAIN WILD-TYPE 92 90 163 133

Figure S64.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.13

Table S65.  Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
9Q GAIN MUTATED 21 3 19
9Q GAIN WILD-TYPE 221 127 188

Figure S65.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0042

Table S66.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
10P GAIN MUTATED 73 44 23 43
10P GAIN WILD-TYPE 103 68 95 108

Figure S66.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.12

Table S67.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
10P GAIN MUTATED 90 53 40
10P GAIN WILD-TYPE 220 105 49

Figure S67.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S68.  Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
10P GAIN MUTATED 119 29 41
10P GAIN WILD-TYPE 123 101 166

Figure S68.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S69.  Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
10P GAIN MUTATED 48 38 23 76
10P GAIN WILD-TYPE 65 60 164 94

Figure S69.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.02

Table S70.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
10P GAIN MUTATED 14 45 40
10P GAIN WILD-TYPE 65 64 72

Figure S70.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0062

Table S71.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
10P GAIN MUTATED 22 27 71 27
10P GAIN WILD-TYPE 83 44 94 79

Figure S71.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MRNA_CNMF'

P value = 0.00516 (Fisher's exact test), Q value = 0.042

Table S72.  Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
10Q GAIN MUTATED 46 24 17 18
10Q GAIN WILD-TYPE 130 88 101 133

Figure S72.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.15

Table S73.  Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
10Q GAIN MUTATED 51 28 26
10Q GAIN WILD-TYPE 259 130 63

Figure S73.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q gain' versus 'MIR_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.2

Table S74.  Gene #20: '10q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
10Q GAIN MUTATED 24 30 51
10Q GAIN WILD-TYPE 157 101 192

Figure S74.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.057

Table S75.  Gene #20: '10q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
10Q GAIN MUTATED 60 17 32
10Q GAIN WILD-TYPE 182 113 175

Figure S75.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S76.  Gene #20: '10q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
10Q GAIN MUTATED 27 28 14 37
10Q GAIN WILD-TYPE 86 70 173 133

Figure S76.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.1

Table S77.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
10Q GAIN MUTATED 7 27 20
10Q GAIN WILD-TYPE 72 82 92

Figure S77.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.21

Table S78.  Gene #21: '11p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
11P GAIN MUTATED 38 9 26
11P GAIN WILD-TYPE 204 121 181

Figure S78.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #5: 'CN_CNMF'

'11p gain' versus 'RPPA_CNMF'

P value = 0.00963 (Fisher's exact test), Q value = 0.069

Table S79.  Gene #21: '11p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
11P GAIN MUTATED 8 29 11
11P GAIN WILD-TYPE 138 160 65

Figure S79.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0026

Table S80.  Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
11Q GAIN MUTATED 57 10 47
11Q GAIN WILD-TYPE 185 120 160

Figure S80.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.03

Table S81.  Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
11Q GAIN MUTATED 26 9 32 45
11Q GAIN WILD-TYPE 87 89 155 125

Figure S81.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00047

Table S82.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
12P GAIN MUTATED 104 45 38 57
12P GAIN WILD-TYPE 72 67 80 94

Figure S82.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0026 (Fisher's exact test), Q value = 0.026

Table S83.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
12P GAIN MUTATED 133 58 53
12P GAIN WILD-TYPE 177 100 36

Figure S83.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.013

Table S84.  Gene #23: '12p gain' 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
12P GAIN MUTATED 33 21 28 36 16 30 19 11 37 12
12P GAIN WILD-TYPE 52 36 30 46 18 45 15 25 15 30

Figure S84.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S85.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
12P GAIN MUTATED 155 38 64
12P GAIN WILD-TYPE 87 92 143

Figure S85.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S86.  Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
12P GAIN MUTATED 58 57 43 93
12P GAIN WILD-TYPE 55 41 144 77

Figure S86.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0039

Table S87.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
12P GAIN MUTATED 22 62 45
12P GAIN WILD-TYPE 57 47 67

Figure S87.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.011

Table S88.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
12P GAIN MUTATED 54 38 37
12P GAIN WILD-TYPE 92 21 58

Figure S88.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0039

Table S89.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
12P GAIN MUTATED 27 38 81 47
12P GAIN WILD-TYPE 78 33 84 59

Figure S89.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MRNA_CNMF'

P value = 0.00566 (Fisher's exact test), Q value = 0.046

Table S90.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
12Q GAIN MUTATED 71 33 27 39
12Q GAIN WILD-TYPE 105 79 91 112

Figure S90.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S91.  Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
12Q GAIN MUTATED 111 30 37
12Q GAIN WILD-TYPE 131 100 170

Figure S91.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S92.  Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
12Q GAIN MUTATED 45 38 26 67
12Q GAIN WILD-TYPE 68 60 161 103

Figure S92.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.15

Table S93.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
12Q GAIN MUTATED 20 46 32
12Q GAIN WILD-TYPE 59 63 80

Figure S93.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.19

Table S94.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
12Q GAIN MUTATED 46 27 25
12Q GAIN WILD-TYPE 100 32 70

Figure S94.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0087 (Fisher's exact test), Q value = 0.064

Table S95.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
12Q GAIN MUTATED 19 28 55 34
12Q GAIN WILD-TYPE 86 43 110 72

Figure S95.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.16

Table S96.  Gene #24: '12q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 6 5 5
12Q GAIN MUTATED 2 0 1 4
12Q GAIN WILD-TYPE 4 6 4 1

Figure S96.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.028

Table S97.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
13Q GAIN MUTATED 25 17 10 6
13Q GAIN WILD-TYPE 151 95 108 145

Figure S97.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.003

Table S98.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
13Q GAIN MUTATED 19 20 19
13Q GAIN WILD-TYPE 291 138 70

Figure S98.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.099

Table S99.  Gene #25: '13q gain' 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
13Q GAIN MUTATED 6 8 5 6 2 10 9 1 9 1
13Q GAIN WILD-TYPE 79 49 53 76 32 65 25 35 43 41

Figure S99.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00085

Table S100.  Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
13Q GAIN MUTATED 40 13 8
13Q GAIN WILD-TYPE 202 117 199

Figure S100.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0081

Table S101.  Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
13Q GAIN MUTATED 15 19 8 18
13Q GAIN WILD-TYPE 98 79 179 152

Figure S101.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.16

Table S102.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
13Q GAIN MUTATED 3 15 16
13Q GAIN WILD-TYPE 76 94 96

Figure S102.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.13

Table S103.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
16P GAIN MUTATED 22 6 19 11
16P GAIN WILD-TYPE 154 106 99 140

Figure S103.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00502 (Fisher's exact test), Q value = 0.042

Table S104.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
16P GAIN MUTATED 34 8 16
16P GAIN WILD-TYPE 276 150 73

Figure S104.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.099

Table S105.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
16Q GAIN MUTATED 10 1 12 8
16Q GAIN WILD-TYPE 166 111 106 143

Figure S105.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.14

Table S106.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
16Q GAIN MUTATED 20 3 8
16Q GAIN WILD-TYPE 290 155 81

Figure S106.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.15

Table S107.  Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
16Q GAIN MUTATED 1 3 13 5
16Q GAIN WILD-TYPE 70 132 128 95

Figure S107.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.16

Table S108.  Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
16Q GAIN MUTATED 2 7 5 8
16Q GAIN WILD-TYPE 103 64 160 98

Figure S108.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIR_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.18

Table S109.  Gene #30: '17p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
17P GAIN MUTATED 2 8 10
17P GAIN WILD-TYPE 179 123 233

Figure S109.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'17p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.17

Table S110.  Gene #30: '17p gain' 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
17P GAIN MUTATED 1 1 1 2 0 2 1 2 7 3
17P GAIN WILD-TYPE 84 56 57 80 34 73 33 34 45 39

Figure S110.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.099

Table S111.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
17Q GAIN MUTATED 15 13 2 10
17Q GAIN WILD-TYPE 161 99 116 141

Figure S111.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00655 (Fisher's exact test), Q value = 0.052

Table S112.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
17Q GAIN MUTATED 13 16 11
17Q GAIN WILD-TYPE 297 142 78

Figure S112.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.012

Table S113.  Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
18P GAIN MUTATED 67 17 35
18P GAIN WILD-TYPE 175 113 172

Figure S113.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S114.  Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
18P GAIN MUTATED 32 20 16 49
18P GAIN WILD-TYPE 81 78 171 121

Figure S114.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.17

Table S115.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
18P GAIN MUTATED 8 27 21
18P GAIN WILD-TYPE 71 82 91

Figure S115.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.097

Table S116.  Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
18Q GAIN MUTATED 39 9 19
18Q GAIN WILD-TYPE 203 121 188

Figure S116.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.071

Table S117.  Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
18Q GAIN MUTATED 15 13 11 28
18Q GAIN WILD-TYPE 98 85 176 142

Figure S117.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S118.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
19P GAIN MUTATED 97 21 52
19P GAIN WILD-TYPE 145 109 155

Figure S118.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00593 (Fisher's exact test), Q value = 0.047

Table S119.  Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
19P GAIN MUTATED 35 28 39 64
19P GAIN WILD-TYPE 78 70 148 106

Figure S119.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S120.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
19Q GAIN MUTATED 97 20 46
19Q GAIN WILD-TYPE 145 110 161

Figure S120.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.021

Table S121.  Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
19Q GAIN MUTATED 39 31 34 56
19Q GAIN WILD-TYPE 74 67 153 114

Figure S121.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S122.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
20P GAIN MUTATED 111 58 41 65
20P GAIN WILD-TYPE 65 54 77 86

Figure S122.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.011

Table S123.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
20P GAIN MUTATED 145 70 60
20P GAIN WILD-TYPE 165 88 29

Figure S123.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0026

Table S124.  Gene #36: '20p gain' 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
20P GAIN MUTATED 31 27 32 36 22 41 25 15 33 12
20P GAIN WILD-TYPE 54 30 26 46 12 34 9 21 19 30

Figure S124.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S125.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
20P GAIN MUTATED 175 36 76
20P GAIN WILD-TYPE 67 94 131

Figure S125.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S126.  Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
20P GAIN MUTATED 64 60 48 108
20P GAIN WILD-TYPE 49 38 139 62

Figure S126.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.074

Table S127.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
20P GAIN MUTATED 32 68 56
20P GAIN WILD-TYPE 47 41 56

Figure S127.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.18

Table S128.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
20P GAIN MUTATED 68 39 49
20P GAIN WILD-TYPE 78 20 46

Figure S128.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00666 (Fisher's exact test), Q value = 0.052

Table S129.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
20P GAIN MUTATED 41 42 96 49
20P GAIN WILD-TYPE 64 29 69 57

Figure S129.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S130.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
20Q GAIN MUTATED 125 70 43 74
20Q GAIN WILD-TYPE 51 42 75 77

Figure S130.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.0089

Table S131.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
20Q GAIN MUTATED 161 85 66
20Q GAIN WILD-TYPE 149 73 23

Figure S131.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0024

Table S132.  Gene #37: '20q gain' 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
20Q GAIN MUTATED 35 30 34 40 25 41 25 20 42 19
20Q GAIN WILD-TYPE 50 27 24 42 9 34 9 16 10 23

Figure S132.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S133.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
20Q GAIN MUTATED 190 39 97
20Q GAIN WILD-TYPE 52 91 110

Figure S133.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S134.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
20Q GAIN MUTATED 74 67 55 122
20Q GAIN WILD-TYPE 39 31 132 48

Figure S134.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.21

Table S135.  Gene #37: '20q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
20Q GAIN MUTATED 88 26 39 76
20Q GAIN WILD-TYPE 55 28 21 78

Figure S135.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00874 (Fisher's exact test), Q value = 0.064

Table S136.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
20Q GAIN MUTATED 75 44 57
20Q GAIN WILD-TYPE 71 15 38

Figure S136.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00781 (Fisher's exact test), Q value = 0.058

Table S137.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
20Q GAIN MUTATED 49 47 107 56
20Q GAIN WILD-TYPE 56 24 58 50

Figure S137.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.008

Table S138.  Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
21Q GAIN MUTATED 61 13 33
21Q GAIN WILD-TYPE 181 117 174

Figure S138.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.02

Table S139.  Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
21Q GAIN MUTATED 30 16 21 40
21Q GAIN WILD-TYPE 83 82 166 130

Figure S139.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.095

Table S140.  Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
21Q GAIN MUTATED 24 23 24 15
21Q GAIN WILD-TYPE 47 112 117 85

Figure S140.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.18

Table S141.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
XP GAIN MUTATED 41 10 27
XP GAIN WILD-TYPE 201 120 180

Figure S141.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0021

Table S142.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
XQ GAIN MUTATED 62 11 35
XQ GAIN WILD-TYPE 180 119 172

Figure S142.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'CN_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0051

Table S143.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
1P LOSS MUTATED 30 9 20
1P LOSS WILD-TYPE 280 149 69

Figure S143.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.15

Table S144.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
2P LOSS MUTATED 38 10 4
2P LOSS WILD-TYPE 272 148 85

Figure S144.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S145.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
3P LOSS MUTATED 46 22 3 25
3P LOSS WILD-TYPE 130 90 115 126

Figure S145.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0087

Table S146.  Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
3P LOSS MUTATED 39 30 27
3P LOSS WILD-TYPE 271 128 62

Figure S146.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0092

Table S147.  Gene #46: '3p loss' 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
3P LOSS MUTATED 16 4 3 13 5 13 13 8 16 5
3P LOSS WILD-TYPE 69 53 55 69 29 62 21 28 36 37

Figure S147.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S148.  Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
3P LOSS MUTATED 62 16 19
3P LOSS WILD-TYPE 180 114 188

Figure S148.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S149.  Gene #46: '3p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
3P LOSS MUTATED 26 21 11 38
3P LOSS WILD-TYPE 87 77 176 132

Figure S149.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.17

Table S150.  Gene #46: '3p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
3P LOSS MUTATED 19 8 17 19
3P LOSS WILD-TYPE 124 46 43 135

Figure S150.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.015

Table S151.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
3P LOSS MUTATED 15 18 21
3P LOSS WILD-TYPE 131 41 74

Figure S151.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 0.00812 (Fisher's exact test), Q value = 0.06

Table S152.  Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
3Q LOSS MUTATED 20 12 3 7
3Q LOSS WILD-TYPE 156 100 115 144

Figure S152.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00993 (Fisher's exact test), Q value = 0.07

Table S153.  Gene #47: '3q loss' 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
3Q LOSS MUTATED 7 1 0 8 1 6 7 3 7 2
3Q LOSS WILD-TYPE 78 56 58 74 33 69 27 33 45 40

Figure S153.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.1

Table S154.  Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
3Q LOSS MUTATED 26 8 8
3Q LOSS WILD-TYPE 216 122 199

Figure S154.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0055

Table S155.  Gene #47: '3q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
3Q LOSS MUTATED 14 9 3 16
3Q LOSS WILD-TYPE 99 89 184 154

Figure S155.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.16

Table S156.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
3Q LOSS MUTATED 6 8 10
3Q LOSS WILD-TYPE 140 51 85

Figure S156.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.011

Table S157.  Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
3Q LOSS MUTATED 4 7 20 1
3Q LOSS WILD-TYPE 101 64 145 105

Figure S157.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.2

Table S158.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
4P LOSS MUTATED 175 73 54
4P LOSS WILD-TYPE 135 85 35

Figure S158.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0029

Table S159.  Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
4P LOSS MUTATED 156 65 94
4P LOSS WILD-TYPE 86 65 113

Figure S159.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

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

Table S160.  Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
4Q LOSS MUTATED 177 79 107
4Q LOSS WILD-TYPE 65 51 100

Figure S160.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.2

Table S161.  Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
5P LOSS MUTATED 68 32 30
5P LOSS WILD-TYPE 242 126 59

Figure S161.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0092

Table S162.  Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
5P LOSS MUTATED 75 22 37
5P LOSS WILD-TYPE 167 108 170

Figure S162.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.082

Table S163.  Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
5P LOSS MUTATED 22 22 33 54
5P LOSS WILD-TYPE 91 76 154 116

Figure S163.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.018

Table S164.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
5P LOSS MUTATED 13 41 23
5P LOSS WILD-TYPE 66 68 89

Figure S164.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.032

Table S165.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
5P LOSS MUTATED 35 25 17
5P LOSS WILD-TYPE 111 34 78

Figure S165.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0499 (Fisher's exact test), Q value = 0.21

Table S166.  Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
5P LOSS MUTATED 24 27 40 21
5P LOSS WILD-TYPE 81 44 125 85

Figure S166.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0049

Table S167.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
5Q LOSS MUTATED 93 37 38 51
5Q LOSS WILD-TYPE 83 75 80 100

Figure S167.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.019

Table S168.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
5Q LOSS MUTATED 115 54 50
5Q LOSS WILD-TYPE 195 104 39

Figure S168.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.084

Table S169.  Gene #51: '5q loss' 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
5Q LOSS MUTATED 30 20 23 28 14 24 22 15 30 13
5Q LOSS WILD-TYPE 55 37 35 54 20 51 12 21 22 29

Figure S169.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00066

Table S170.  Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
5Q LOSS MUTATED 123 36 69
5Q LOSS WILD-TYPE 119 94 138

Figure S170.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S171.  Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
5Q LOSS MUTATED 42 34 53 95
5Q LOSS WILD-TYPE 71 64 134 75

Figure S171.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.013

Table S172.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
5Q LOSS MUTATED 24 59 38
5Q LOSS WILD-TYPE 55 50 74

Figure S172.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00254 (Fisher's exact test), Q value = 0.026

Table S173.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
5Q LOSS MUTATED 56 35 30
5Q LOSS WILD-TYPE 90 24 65

Figure S173.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.036

Table S174.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
5Q LOSS MUTATED 38 36 79 31
5Q LOSS WILD-TYPE 67 35 86 75

Figure S174.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.16

Table S175.  Gene #53: '6q loss' 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
6Q LOSS MUTATED 39 29 27 28 10 39 16 17 13 15
6Q LOSS WILD-TYPE 46 28 31 54 24 36 18 19 39 27

Figure S175.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.1

Table S176.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
6Q LOSS MUTATED 60 15 46
6Q LOSS WILD-TYPE 86 44 49

Figure S176.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.12

Table S177.  Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
7P LOSS MUTATED 41 23 14 40
7P LOSS WILD-TYPE 135 89 104 111

Figure S177.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q loss' versus 'MRNA_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.13

Table S178.  Gene #55: '7q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
7Q LOSS MUTATED 29 18 7 25
7Q LOSS WILD-TYPE 147 94 111 126

Figure S178.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.038

Table S179.  Gene #56: '8p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
8P LOSS MUTATED 54 46 70 96
8P LOSS WILD-TYPE 59 52 117 74

Figure S179.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.16

Table S180.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
8P LOSS MUTATED 35 37 80 52
8P LOSS WILD-TYPE 70 34 85 54

Figure S180.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MRNA_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.15

Table S181.  Gene #57: '8q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
8Q LOSS MUTATED 39 12 17 18
8Q LOSS WILD-TYPE 137 100 101 133

Figure S181.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00269 (Fisher's exact test), Q value = 0.026

Table S182.  Gene #57: '8q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
8Q LOSS MUTATED 42 19 25
8Q LOSS WILD-TYPE 268 139 64

Figure S182.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00263 (Fisher's exact test), Q value = 0.026

Table S183.  Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
8Q LOSS MUTATED 53 13 25
8Q LOSS WILD-TYPE 189 117 182

Figure S183.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.026

Table S184.  Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
8Q LOSS MUTATED 12 23 19 35
8Q LOSS WILD-TYPE 101 75 168 135

Figure S184.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.00946 (Fisher's exact test), Q value = 0.068

Table S185.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
8Q LOSS MUTATED 7 27 15
8Q LOSS WILD-TYPE 72 82 97

Figure S185.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.026

Table S186.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
8Q LOSS MUTATED 18 19 12
8Q LOSS WILD-TYPE 128 40 83

Figure S186.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.089

Table S187.  Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
8Q LOSS MUTATED 8 18 27 15
8Q LOSS WILD-TYPE 97 53 138 91

Figure S187.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.013

Table S188.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
9P LOSS MUTATED 91 60 49 50
9P LOSS WILD-TYPE 85 52 69 101

Figure S188.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.033

Table S189.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
9P LOSS MUTATED 126 70 54
9P LOSS WILD-TYPE 184 88 35

Figure S189.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.17

Table S190.  Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
9P LOSS MUTATED 122 62 80
9P LOSS WILD-TYPE 120 68 127

Figure S190.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.01

Table S191.  Gene #58: '9p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
9P LOSS MUTATED 59 54 63 81
9P LOSS WILD-TYPE 54 44 124 89

Figure S191.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.16

Table S192.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
9Q LOSS MUTATED 99 57 55 61
9Q LOSS WILD-TYPE 77 55 63 90

Figure S192.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00738 (Fisher's exact test), Q value = 0.057

Table S193.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
9Q LOSS MUTATED 144 71 57
9Q LOSS WILD-TYPE 166 87 32

Figure S193.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.14

Table S194.  Gene #59: '9q loss' 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
9Q LOSS MUTATED 31 30 35 33 21 33 21 18 31 19
9Q LOSS WILD-TYPE 54 27 23 49 13 42 13 18 21 23

Figure S194.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S195.  Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
9Q LOSS MUTATED 153 62 72
9Q LOSS WILD-TYPE 89 68 135

Figure S195.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S196.  Gene #59: '9q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
9Q LOSS MUTATED 63 55 59 103
9Q LOSS WILD-TYPE 50 43 128 67

Figure S196.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00354 (Fisher's exact test), Q value = 0.032

Table S197.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
9Q LOSS MUTATED 27 64 51
9Q LOSS WILD-TYPE 52 45 61

Figure S197.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.016

Table S198.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
9Q LOSS MUTATED 59 40 43
9Q LOSS WILD-TYPE 87 19 52

Figure S198.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.15

Table S199.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
9Q LOSS MUTATED 38 39 86 55
9Q LOSS WILD-TYPE 67 32 79 51

Figure S199.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIR_CNMF'

P value = 0.00586 (Fisher's exact test), Q value = 0.047

Table S200.  Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
10Q LOSS MUTATED 44 16 62
10Q LOSS WILD-TYPE 137 115 181

Figure S200.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00066

Table S201.  Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
10Q LOSS MUTATED 77 15 35
10Q LOSS WILD-TYPE 165 115 172

Figure S201.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.19

Table S202.  Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
10Q LOSS MUTATED 22 19 34 51
10Q LOSS WILD-TYPE 91 79 153 119

Figure S202.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p loss' versus 'MRNA_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.13

Table S203.  Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
11P LOSS MUTATED 75 35 31 49
11P LOSS WILD-TYPE 101 77 87 102

Figure S203.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00925 (Fisher's exact test), Q value = 0.067

Table S204.  Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
11P LOSS MUTATED 92 56 42
11P LOSS WILD-TYPE 218 102 47

Figure S204.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.042

Table S205.  Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
11P LOSS MUTATED 102 38 60
11P LOSS WILD-TYPE 140 92 147

Figure S205.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.03

Table S206.  Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
11P LOSS MUTATED 40 40 45 69
11P LOSS WILD-TYPE 73 58 142 101

Figure S206.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.15

Table S207.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
11P LOSS MUTATED 18 52 42 44
11P LOSS WILD-TYPE 53 83 99 56

Figure S207.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.011

Table S208.  Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
11Q LOSS MUTATED 81 25 41
11Q LOSS WILD-TYPE 161 105 166

Figure S208.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.037

Table S209.  Gene #63: '11q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
11Q LOSS MUTATED 34 30 30 49
11Q LOSS WILD-TYPE 79 68 157 121

Figure S209.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.099

Table S210.  Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
11Q LOSS MUTATED 12 39 30 36
11Q LOSS WILD-TYPE 59 96 111 64

Figure S210.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'12p loss' versus 'MRNA_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.055

Table S211.  Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
12P LOSS MUTATED 13 23 20 21
12P LOSS WILD-TYPE 163 89 98 130

Figure S211.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.078

Table S212.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
12P LOSS MUTATED 42 30 5
12P LOSS WILD-TYPE 268 128 84

Figure S212.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.071

Table S213.  Gene #64: '12p loss' 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
12P LOSS MUTATED 12 11 7 11 4 12 1 11 1 7
12P LOSS WILD-TYPE 73 46 51 71 30 63 33 25 51 35

Figure S213.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S214.  Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
12P LOSS MUTATED 15 18 46
12P LOSS WILD-TYPE 227 112 161

Figure S214.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0065

Table S215.  Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
12P LOSS MUTATED 5 30 10 19
12P LOSS WILD-TYPE 66 105 131 81

Figure S215.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00613 (Fisher's exact test), Q value = 0.049

Table S216.  Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
12P LOSS MUTATED 24 5 26 9
12P LOSS WILD-TYPE 81 66 139 97

Figure S216.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.072

Table S217.  Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
12Q LOSS MUTATED 37 18 52
12Q LOSS WILD-TYPE 205 112 155

Figure S217.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.17

Table S218.  Gene #65: '12q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
12Q LOSS MUTATED 31 24 18
12Q LOSS WILD-TYPE 115 165 58

Figure S218.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.098

Table S219.  Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
12Q LOSS MUTATED 12 34 15 20
12Q LOSS WILD-TYPE 59 101 126 80

Figure S219.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00431 (Fisher's exact test), Q value = 0.037

Table S220.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
13Q LOSS MUTATED 182 77 36
13Q LOSS WILD-TYPE 128 81 53

Figure S220.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.11

Table S221.  Gene #66: '13q loss' 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
13Q LOSS MUTATED 46 29 38 49 18 30 13 26 24 23
13Q LOSS WILD-TYPE 39 28 20 33 16 45 21 10 28 19

Figure S221.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00344 (Fisher's exact test), Q value = 0.032

Table S222.  Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
13Q LOSS MUTATED 129 54 125
13Q LOSS WILD-TYPE 113 76 82

Figure S222.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.019

Table S223.  Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
13Q LOSS MUTATED 70 36 101 96
13Q LOSS WILD-TYPE 43 62 86 74

Figure S223.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.14

Table S224.  Gene #66: '13q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
13Q LOSS MUTATED 64 111 40
13Q LOSS WILD-TYPE 82 78 36

Figure S224.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.14

Table S225.  Gene #66: '13q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
13Q LOSS MUTATED 63 29 40 83
13Q LOSS WILD-TYPE 80 25 20 71

Figure S225.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S226.  Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
14Q LOSS MUTATED 124 36 57
14Q LOSS WILD-TYPE 118 94 150

Figure S226.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.024

Table S227.  Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
14Q LOSS MUTATED 43 41 50 77
14Q LOSS WILD-TYPE 70 57 137 93

Figure S227.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.0042 (Fisher's exact test), Q value = 0.037

Table S228.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
14Q LOSS MUTATED 19 51 37
14Q LOSS WILD-TYPE 60 58 75

Figure S228.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S229.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
14Q LOSS MUTATED 36 36 35
14Q LOSS WILD-TYPE 110 23 60

Figure S229.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0089

Table S230.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
15Q LOSS MUTATED 106 48 44 73
15Q LOSS WILD-TYPE 70 64 74 78

Figure S230.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.099

Table S231.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
15Q LOSS MUTATED 151 66 54
15Q LOSS WILD-TYPE 159 92 35

Figure S231.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'MIR_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0056

Table S232.  Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
15Q LOSS MUTATED 76 53 142
15Q LOSS WILD-TYPE 105 78 101

Figure S232.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'15q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0029

Table S233.  Gene #68: '15q loss' 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
15Q LOSS MUTATED 26 27 35 41 18 42 23 18 30 11
15Q LOSS WILD-TYPE 59 30 23 41 16 33 11 18 22 31

Figure S233.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S234.  Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
15Q LOSS MUTATED 169 37 75
15Q LOSS WILD-TYPE 73 93 132

Figure S234.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S235.  Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
15Q LOSS MUTATED 54 50 61 113
15Q LOSS WILD-TYPE 59 48 126 57

Figure S235.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.094

Table S236.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
15Q LOSS MUTATED 28 62 51
15Q LOSS WILD-TYPE 51 47 61

Figure S236.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.098

Table S237.  Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
15Q LOSS MUTATED 29 80 62 56
15Q LOSS WILD-TYPE 42 55 79 44

Figure S237.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.011

Table S238.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
15Q LOSS MUTATED 43 37 103 44
15Q LOSS WILD-TYPE 62 34 62 62

Figure S238.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.13

Table S239.  Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
16P LOSS MUTATED 155 65 115
16P LOSS WILD-TYPE 87 65 92

Figure S239.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.14

Table S240.  Gene #69: '16p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
16P LOSS MUTATED 71 58 92 108
16P LOSS WILD-TYPE 42 40 95 62

Figure S240.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.14

Table S241.  Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
16P LOSS MUTATED 65 33 109 58
16P LOSS WILD-TYPE 40 38 56 48

Figure S241.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIR_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.064

Table S242.  Gene #70: '16q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
16Q LOSS MUTATED 134 79 182
16Q LOSS WILD-TYPE 47 52 61

Figure S242.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00066

Table S243.  Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
16Q LOSS MUTATED 193 74 146
16Q LOSS WILD-TYPE 49 56 61

Figure S243.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.006

Table S244.  Gene #70: '16q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
16Q LOSS MUTATED 90 72 112 131
16Q LOSS WILD-TYPE 23 26 75 39

Figure S244.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.13

Table S245.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
16Q LOSS MUTATED 47 108 93 77
16Q LOSS WILD-TYPE 24 27 48 23

Figure S245.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.1

Table S246.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
17Q LOSS MUTATED 223 94 56
17Q LOSS WILD-TYPE 87 64 33

Figure S246.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.1

Table S247.  Gene #72: '17q loss' 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
17Q LOSS MUTATED 51 38 44 59 19 49 30 26 27 29
17Q LOSS WILD-TYPE 34 19 14 23 15 26 4 10 25 13

Figure S247.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.0046 (Fisher's exact test), Q value = 0.039

Table S248.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
17Q LOSS MUTATED 64 72 66
17Q LOSS WILD-TYPE 15 37 46

Figure S248.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'18p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.13

Table S249.  Gene #73: '18p loss' 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
18P LOSS MUTATED 37 16 20 26 21 39 12 17 21 18
18P LOSS WILD-TYPE 48 41 38 56 13 36 22 19 31 24

Figure S249.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.2

Table S250.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
18P LOSS MUTATED 49 27 46
18P LOSS WILD-TYPE 97 32 49

Figure S250.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.11

Table S251.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
18Q LOSS MUTATED 62 37 52
18Q LOSS WILD-TYPE 84 22 43

Figure S251.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.19

Table S252.  Gene #75: '19p loss' 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
19P LOSS MUTATED 24 16 21 32 8 19 17 10 12 20
19P LOSS WILD-TYPE 61 41 37 50 26 56 17 26 40 22

Figure S252.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19p loss' versus 'RPPA_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.15

Table S253.  Gene #75: '19p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
19P LOSS MUTATED 36 57 32
19P LOSS WILD-TYPE 110 132 44

Figure S253.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.15

Table S254.  Gene #75: '19p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
19P LOSS MUTATED 35 25 20 45
19P LOSS WILD-TYPE 108 29 40 109

Figure S254.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.17

Table S255.  Gene #75: '19p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 6 5 5
19P LOSS MUTATED 2 0 3 4
19P LOSS WILD-TYPE 4 6 2 1

Figure S255.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.098

Table S256.  Gene #76: '19q loss' 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
19Q LOSS MUTATED 26 16 18 31 7 18 17 9 8 18
19Q LOSS WILD-TYPE 59 41 40 51 27 57 17 27 44 24

Figure S256.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00778 (Fisher's exact test), Q value = 0.058

Table S257.  Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
19Q LOSS MUTATED 79 49 47
19Q LOSS WILD-TYPE 163 81 160

Figure S257.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

'20q loss' versus 'MIR_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.19

Table S258.  Gene #78: '20q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
20Q LOSS MUTATED 13 2 16
20Q LOSS WILD-TYPE 168 129 227

Figure S258.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.16

Table S259.  Gene #79: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
21Q LOSS MUTATED 99 42 61
21Q LOSS WILD-TYPE 143 88 146

Figure S259.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.15

Table S260.  Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
21Q LOSS MUTATED 30 38 58 71
21Q LOSS WILD-TYPE 83 60 129 99

Figure S260.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0076

Table S261.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
22Q LOSS MUTATED 149 81 85 98
22Q LOSS WILD-TYPE 27 31 33 53

Figure S261.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MIR_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.071

Table S262.  Gene #80: '22q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
22Q LOSS MUTATED 131 87 195
22Q LOSS WILD-TYPE 50 44 48

Figure S262.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S263.  Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
22Q LOSS MUTATED 206 87 138
22Q LOSS WILD-TYPE 36 43 69

Figure S263.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0016

Table S264.  Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
22Q LOSS MUTATED 89 85 118 129
22Q LOSS WILD-TYPE 24 13 69 41

Figure S264.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.072

Table S265.  Gene #80: '22q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
22Q LOSS MUTATED 105 152 48
22Q LOSS WILD-TYPE 41 37 28

Figure S265.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.19

Table S266.  Gene #80: '22q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
22Q LOSS MUTATED 97 37 46 125
22Q LOSS WILD-TYPE 46 17 14 29

Figure S266.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.1

Table S267.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
22Q LOSS MUTATED 102 52 70
22Q LOSS WILD-TYPE 44 7 25

Figure S267.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00767 (Fisher's exact test), Q value = 0.058

Table S268.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
XP LOSS MUTATED 50 55 121 98
XP LOSS WILD-TYPE 63 43 66 72

Figure S268.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.091

Table S269.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
XP LOSS MUTATED 65 34 39 93
XP LOSS WILD-TYPE 78 20 21 61

Figure S269.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.13

Table S270.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
XP LOSS MUTATED 31 78 87 66
XP LOSS WILD-TYPE 40 57 54 34

Figure S270.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.094

Table S271.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
XQ LOSS MUTATED 102 72 111
XQ LOSS WILD-TYPE 140 58 96

Figure S271.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.015

Table S272.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
XQ LOSS MUTATED 44 48 113 77
XQ LOSS WILD-TYPE 69 50 74 93

Figure S272.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.19

Table S273.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
XQ LOSS MUTATED 56 31 34 74
XQ LOSS WILD-TYPE 87 23 26 80

Figure S273.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/22534547/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/22555032/OV-TP.transferedmergedcluster.txt

  • Number of patients = 579

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 14

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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