Correlation between copy number variations of arm-level result and molecular subtypes
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 79 arm-level events and 12 molecular subtypes across 463 patients, 145 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 2p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 2q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 3q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 5p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

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

  • 10q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF'.

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

  • 18q gain cnv correlated to 'MRNASEQ_CNMF'.

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

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

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

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

  • xq gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 2p loss cnv correlated to 'CN_CNMF'.

  • 2q loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 3q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 4p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 8q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 13q loss cnv correlated to 'CN_CNMF'.

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

  • 15q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 16p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

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

  • xq loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 145 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
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 Chi-square test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test
1p loss 168 (36%) 295 0.0286
(1.00) 		0.000173
(0.123) 		6.36e-47
(5.3e-44) 		4.6e-95
(3.87e-92) 		0.000311
(0.217) 		0.142
(1.00) 		9.13e-52
(7.64e-49) 		9.06e-65
(7.59e-62) 		1.7e-22
(1.39e-19) 		2.08e-06
(0.00157) 		7.07e-27
(5.82e-24) 		0.000124
(0.089)
10p loss 76 (16%) 387 0.271
(1.00) 		0.561
(1.00) 		4.58e-40
(3.79e-37) 		2.75e-49
(2.3e-46) 		2.54e-07
(0.000194) 		0.00232
(1.00) 		2.15e-37
(1.78e-34) 		1.09e-08
(8.56e-06) 		1.58e-15
(1.29e-12) 		2.8e-05
(0.0207) 		1.13e-28
(9.29e-26) 		0.00143
(0.956)
10q loss 91 (20%) 372 0.271
(1.00) 		0.561
(1.00) 		1.47e-33
(1.22e-30) 		2.75e-40
(2.29e-37) 		1.32e-06
(0.000999) 		0.000874
(0.596) 		2.76e-35
(2.28e-32) 		4.69e-11
(3.74e-08) 		2.76e-16
(2.25e-13) 		4.17e-06
(0.00312) 		1.19e-25
(9.76e-23) 		0.00156
(1.00)
19q loss 190 (41%) 273 0.183
(1.00) 		0.159
(1.00) 		1.11e-35
(9.18e-33) 		1.07e-75
(8.96e-73) 		0.0384
(1.00) 		0.118
(1.00) 		6.85e-42
(5.69e-39) 		1.33e-49
(1.11e-46) 		1.83e-16
(1.49e-13) 		7.94e-06
(0.00592) 		3e-20
(2.46e-17) 		0.000259
(0.182)
7p gain 117 (25%) 346 0.745
(1.00) 		0.648
(1.00) 		7.33e-48
(6.12e-45) 		5.97e-24
(4.9e-21) 		0.000874
(0.596) 		0.0177
(1.00) 		8.5e-17
(6.95e-14) 		1.32e-06
(0.000999) 		3.53e-08
(2.74e-05) 		0.0017
(1.00) 		6.79e-10
(5.37e-07) 		0.289
(1.00)
7q gain 145 (31%) 318 0.764
(1.00) 		0.495
(1.00) 		3.82e-45
(3.18e-42) 		1.92e-19
(1.57e-16) 		0.00531
(1.00) 		0.0386
(1.00) 		6.94e-12
(5.56e-09) 		6.84e-07
(0.00052) 		2.4e-07
(0.000184) 		0.00202
(1.00) 		1.28e-07
(9.85e-05) 		0.579
(1.00)
19p gain 89 (19%) 374 0.221
(1.00) 		0.836
(1.00) 		1.46e-09
(1.15e-06) 		4.97e-16
(4.05e-13) 		0.616
(1.00) 		0.406
(1.00) 		3.22e-10
(2.56e-07) 		0.000216
(0.152) 		8.46e-05
(0.0616) 		0.549
(1.00) 		5.8e-07
(0.000443) 		0.521
(1.00)
19q gain 24 (5%) 439 6.12e-14
(4.95e-11) 		3.92e-15
(3.18e-12) 		0.0658
(1.00) 		0.187
(1.00) 		7.94e-12
(6.35e-09) 		0.000237
(0.166) 		3.68e-09
(2.9e-06) 		0.00358
(1.00) 		9.72e-11
(7.75e-08) 		0.182
(1.00)
1p gain 12 (3%) 451 9.4e-05
(0.0683) 		3.28e-05
(0.0242) 		0.0241
(1.00) 		1
(1.00) 		7.74e-09
(6.08e-06) 		0.000827
(0.565) 		3.14e-05
(0.0232) 		0.00144
(0.961) 		0.000137
(0.098) 		0.00641
(1.00)
20p gain 42 (9%) 421 5.97e-12
(4.79e-09) 		3.45e-13
(2.79e-10) 		0.00101
(0.681) 		0.158
(1.00) 		7.62e-08
(5.91e-05) 		0.0044
(1.00) 		2.61e-06
(0.00197) 		0.0277
(1.00) 		1.74e-10
(1.38e-07) 		0.213
(1.00)
20q gain 42 (9%) 421 5.97e-12
(4.79e-09) 		5.69e-14
(4.61e-11) 		0.000898
(0.611) 		0.11
(1.00) 		7.14e-10
(5.64e-07) 		0.000673
(0.462) 		6.28e-08
(4.88e-05) 		0.00189
(1.00) 		2.19e-12
(1.77e-09) 		0.0656
(1.00)
8p loss 17 (4%) 446 0.615
(1.00) 		0.00137
(0.916) 		1.5e-05
(0.0112) 		9.6e-05
(0.0697) 		0.0185
(1.00) 		0.628
(1.00) 		2.08e-07
(0.00016) 		0.00347
(1.00) 		2.93e-05
(0.0217) 		0.128
(1.00) 		2.32e-05
(0.0172) 		0.0463
(1.00)
8q loss 11 (2%) 452 0.000142
(0.102) 		1.59e-05
(0.0118) 		0.0806
(1.00) 		0.74
(1.00) 		0.000108
(0.0782) 		0.0214
(1.00) 		0.000285
(0.199) 		0.154
(1.00) 		0.000231
(0.162) 		0.181
(1.00)
22q loss 50 (11%) 413 0.815
(1.00) 		0.106
(1.00) 		7.69e-12
(6.15e-09) 		1.04e-07
(8e-05) 		7.58e-05
(0.0555) 		0.0405
(1.00) 		2.02e-07
(0.000155) 		0.000187
(0.132) 		0.0723
(1.00) 		0.388
(1.00) 		0.00783
(1.00) 		0.0485
(1.00)
1q gain 18 (4%) 445 0.00011
(0.0794) 		0.000131
(0.0939) 		0.436
(1.00) 		0.738
(1.00) 		0.000107
(0.0776) 		0.0513
(1.00) 		0.00894
(1.00) 		0.25
(1.00) 		0.000353
(0.246) 		0.2
(1.00)
10p gain 47 (10%) 416 1
(1.00) 		0.0879
(1.00) 		1.62e-14
(1.32e-11) 		6.13e-13
(4.94e-10) 		0.0233
(1.00) 		0.546
(1.00) 		2.34e-09
(1.85e-06) 		3.55e-06
(0.00267) 		0.0145
(1.00) 		0.582
(1.00) 		0.0161
(1.00) 		0.789
(1.00)
11p loss 56 (12%) 407 1
(1.00) 		0.0138
(1.00) 		5.02e-14
(4.07e-11) 		1.23e-10
(9.77e-08) 		0.0127
(1.00) 		0.59
(1.00) 		5.15e-12
(4.14e-09) 		8.73e-09
(6.84e-06) 		0.00272
(1.00) 		0.0458
(1.00) 		0.00663
(1.00) 		0.00287
(1.00)
4p loss 67 (14%) 396 1
(1.00) 		0.607
(1.00) 		0.0164
(1.00) 		4.77e-10
(3.78e-07) 		0.429
(1.00) 		0.0287
(1.00) 		3.54e-08
(2.75e-05) 		5.94e-07
(0.000452) 		0.0046
(1.00) 		0.0655
(1.00) 		0.00188
(1.00) 		0.676
(1.00)
4q loss 85 (18%) 378 1
(1.00) 		0.196
(1.00) 		0.00385
(1.00) 		8.29e-09
(6.51e-06) 		0.264
(1.00) 		0.0532
(1.00) 		1.27e-07
(9.84e-05) 		8.23e-05
(0.0601) 		0.000763
(0.523) 		0.0145
(1.00) 		0.000405
(0.28) 		0.409
(1.00)
5q loss 29 (6%) 434 0.446
(1.00) 		0.0182
(1.00) 		8.78e-07
(0.000667) 		0.00242
(1.00) 		0.0218
(1.00) 		0.508
(1.00) 		1.67e-07
(0.000129) 		0.00416
(1.00) 		0.062
(1.00) 		0.108
(1.00) 		0.00804
(1.00) 		0.00023
(0.162)
11q loss 19 (4%) 444 0.000202
(0.143) 		0.000147
(0.105) 		0.0179
(1.00) 		1
(1.00) 		8.75e-08
(6.77e-05) 		0.00425
(1.00) 		0.00226
(1.00) 		0.0342
(1.00) 		0.00293
(1.00) 		0.00705
(1.00)
14q loss 70 (15%) 393 0.467
(1.00) 		0.473
(1.00) 		0.000398
(0.276) 		0.000151
(0.108) 		0.0459
(1.00) 		0.148
(1.00) 		5.7e-05
(0.0418) 		0.0115
(1.00) 		0.000628
(0.433) 		0.208
(1.00) 		0.000104
(0.0751) 		0.00529
(1.00)
10q gain 7 (2%) 456 0.000234
(0.165) 		0.233
(1.00) 		0.267
(1.00) 		0.465
(1.00) 		0.000291
(0.203) 		0.54
(1.00) 		0.00745
(1.00) 		0.43
(1.00) 		0.108
(1.00) 		0.73
(1.00)
18p gain 15 (3%) 448 7.9e-05
(0.0577) 		0.0109
(1.00) 		0.0226
(1.00) 		0.205
(1.00) 		1.53e-10
(1.22e-07) 		0.0194
(1.00) 		0.722
(1.00) 		0.118
(1.00) 		0.413
(1.00) 		0.063
(1.00)
xq gain 35 (8%) 428 1.79e-08
(1.4e-05) 		8.22e-07
(0.000625) 		0.239
(1.00) 		0.72
(1.00) 		0.00987
(1.00) 		0.00115
(0.774) 		0.258
(1.00) 		0.341
(1.00) 		0.143
(1.00) 		0.418
(1.00)
9p loss 107 (23%) 356 0.384
(1.00) 		0.27
(1.00) 		4.22e-06
(0.00315) 		0.000274
(0.192) 		0.0318
(1.00) 		0.0664
(1.00) 		0.000944
(0.639) 		0.0288
(1.00) 		0.13
(1.00) 		0.849
(1.00) 		0.248
(1.00) 		0.549
(1.00)
12q loss 47 (10%) 416 1
(1.00) 		0.0879
(1.00) 		2.11e-08
(1.65e-05) 		2.36e-07
(0.000181) 		0.583
(1.00) 		0.613
(1.00) 		0.0365
(1.00) 		0.000386
(0.269) 		0.019
(1.00) 		0.442
(1.00) 		0.0016
(1.00) 		0.605
(1.00)
xq loss 60 (13%) 403 0.839
(1.00) 		0.022
(1.00) 		0.338
(1.00) 		0.000911
(0.618) 		0.0474
(1.00) 		0.00884
(1.00) 		1.05e-05
(0.00779) 		0.000162
(0.115) 		0.00219
(1.00) 		0.931
(1.00) 		0.00499
(1.00) 		0.298
(1.00)
2p gain 11 (2%) 452 0.0489
(1.00) 		0.046
(1.00) 		0.311
(1.00) 		0.43
(1.00) 		1.67e-06
(0.00126) 		0.139
(1.00) 		0.0356
(1.00) 		0.154
(1.00) 		0.0695
(1.00) 		0.181
(1.00)
2q gain 10 (2%) 453 0.0898
(1.00) 		0.0314
(1.00) 		0.311
(1.00) 		0.43
(1.00) 		2.6e-07
(0.000199) 		0.237
(1.00) 		0.0728
(1.00) 		0.21
(1.00) 		0.0909
(1.00) 		0.216
(1.00)
3q gain 8 (2%) 455 0.215
(1.00) 		0.064
(1.00) 		0.056
(1.00) 		0.74
(1.00) 		0.000151
(0.108) 		0.36
(1.00) 		0.135
(1.00) 		0.479
(1.00) 		0.211
(1.00) 		0.362
(1.00)
5p gain 9 (2%) 454 0.00275
(1.00) 		0.00473
(1.00) 		0.0217
(1.00) 		1
(1.00) 		5.71e-05
(0.0419) 		0.0652
(1.00) 		0.00617
(1.00) 		0.107
(1.00) 		0.00594
(1.00) 		0.0152
(1.00)
8p gain 39 (8%) 424 1.15e-05
(0.00857) 		0.014
(1.00) 		0.0667
(1.00) 		0.566
(1.00) 		0.109
(1.00) 		0.102
(1.00) 		0.308
(1.00) 		0.478
(1.00) 		0.296
(1.00) 		0.215
(1.00)
8q gain 49 (11%) 414 0.0519
(1.00) 		0.303
(1.00) 		2e-06
(0.00151) 		0.000651
(0.448) 		0.0129
(1.00) 		0.618
(1.00) 		0.00143
(0.953) 		0.0213
(1.00) 		0.0166
(1.00) 		0.475
(1.00) 		0.0053
(1.00) 		0.189
(1.00)
12p gain 30 (6%) 433 0.754
(1.00) 		0.0879
(1.00) 		0.000206
(0.146) 		0.0764
(1.00) 		0.261
(1.00) 		0.875
(1.00) 		0.143
(1.00) 		0.0621
(1.00) 		0.0297
(1.00) 		0.111
(1.00) 		0.0211
(1.00) 		0.166
(1.00)
18q gain 12 (3%) 451 0.00094
(0.637) 		0.00796
(1.00) 		0.0804
(1.00) 		0.142
(1.00) 		3.48e-08
(2.71e-05) 		0.0214
(1.00) 		0.368
(1.00) 		0.0234
(1.00) 		0.195
(1.00) 		0.0217
(1.00)
2p loss 19 (4%) 444 3.45e-05
(0.0254) 		0.0682
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.11
(1.00) 		0.0233
(1.00) 		0.146
(1.00) 		0.0883
(1.00) 		0.749
(1.00) 		0.00829
(1.00)
2q loss 18 (4%) 445 5.82e-06
(0.00435) 		0.00896
(1.00) 		0.0692
(1.00) 		0.628
(1.00) 		0.0822
(1.00) 		0.00551
(1.00) 		0.682
(1.00) 		0.434
(1.00) 		0.0438
(1.00) 		0.00458
(1.00)
3p loss 25 (5%) 438 0.00255
(1.00) 		0.146
(1.00) 		0.00652
(1.00) 		0.483
(1.00) 		8.6e-05
(0.0626) 		0.00567
(1.00) 		0.0233
(1.00) 		0.165
(1.00) 		0.0298
(1.00) 		0.0377
(1.00)
3q loss 25 (5%) 438 0.175
(1.00) 		0.561
(1.00) 		0.00598
(1.00) 		0.221
(1.00) 		0.258
(1.00) 		0.191
(1.00) 		0.0002
(0.142) 		0.0682
(1.00) 		0.0364
(1.00) 		0.115
(1.00) 		0.151
(1.00) 		0.0377
(1.00)
5p loss 32 (7%) 431 0.745
(1.00) 		0.0422
(1.00) 		3.68e-06
(0.00276) 		0.00107
(0.717) 		0.849
(1.00) 		1
(1.00) 		0.206
(1.00) 		0.046
(1.00) 		0.13
(1.00) 		0.562
(1.00) 		0.613
(1.00) 		0.19
(1.00)
13q loss 104 (22%) 359 0.18
(1.00) 		0.000618
(0.427) 		3.5e-08
(2.73e-05) 		0.027
(1.00) 		0.0263
(1.00) 		0.49
(1.00) 		0.00468
(1.00) 		0.0117
(1.00) 		0.0226
(1.00) 		0.232
(1.00) 		0.0311
(1.00) 		0.0701
(1.00)
15q loss 45 (10%) 418 1
(1.00) 		0.892
(1.00) 		0.0666
(1.00) 		0.000585
(0.405) 		0.277
(1.00) 		0.0476
(1.00) 		0.000104
(0.0755) 		0.00751
(1.00) 		0.0955
(1.00) 		0.518
(1.00) 		0.0867
(1.00) 		0.358
(1.00)
16p loss 13 (3%) 450 0.00321
(1.00) 		0.0608
(1.00) 		0.865
(1.00) 		0.447
(1.00) 		4.53e-05
(0.0333) 		1
(1.00) 		0.39
(1.00) 		1
(1.00) 		0.519
(1.00) 		0.187
(1.00)
20p loss 5 (1%) 458 0.0513
(1.00) 		0.136
(1.00) 		0.792
(1.00) 		1
(1.00) 		1.05e-06
(0.000796) 		0.586
(1.00) 		0.213
(1.00) 		0.225
(1.00) 		0.142
(1.00) 		0.417
(1.00)
21q loss 33 (7%) 430 0.615
(1.00) 		0.407
(1.00) 		0.000159
(0.114) 		0.00221
(1.00) 		0.461
(1.00) 		0.834
(1.00) 		0.0143
(1.00) 		0.000976
(0.66) 		0.212
(1.00) 		0.013
(1.00) 		0.219
(1.00) 		0.074
(1.00)
3p gain 11 (2%) 452 0.351
(1.00) 		0.182
(1.00) 		0.464
(1.00) 		0.447
(1.00) 		0.00772
(1.00) 		0.388
(1.00) 		0.143
(1.00) 		0.481
(1.00) 		0.261
(1.00) 		0.181
(1.00)
4p gain 12 (3%) 451 0.0068
(1.00) 		0.0361
(1.00) 		0.0327
(1.00) 		0.787
(1.00) 		0.00288
(1.00) 		0.0109
(1.00) 		0.0563
(1.00) 		0.154
(1.00) 		0.24
(1.00) 		0.0702
(1.00)
4q gain 5 (1%) 458 0.0513
(1.00) 		0.12
(1.00) 		0.113
(1.00) 		0.668
(1.00) 		0.0185
(1.00) 		0.586
(1.00) 		0.177
(1.00) 		0.485
(1.00) 		0.0303
(1.00) 		0.0359
(1.00)
5q gain 7 (2%) 456 0.00361
(1.00) 		0.00166
(1.00) 		0.0109
(1.00) 		0.242
(1.00) 		0.0115
(1.00) 		0.267
(1.00) 		0.0141
(1.00) 		0.2
(1.00)
6p gain 7 (2%) 456 0.00583
(1.00) 		0.0486
(1.00) 		0.0378
(1.00) 		0.465
(1.00) 		0.127
(1.00) 		0.0307
(1.00) 		0.137
(1.00) 		0.02
(1.00) 		0.0231
(1.00) 		0.2
(1.00)
9p gain 17 (4%) 446 0.00784
(1.00) 		0.145
(1.00) 		0.294
(1.00) 		0.82
(1.00) 		0.0167
(1.00) 		0.354
(1.00) 		0.406
(1.00) 		0.434
(1.00) 		0.126
(1.00) 		0.243
(1.00)
9q gain 22 (5%) 441 0.00339
(1.00) 		0.219
(1.00) 		0.258
(1.00) 		0.661
(1.00) 		0.00222
(1.00) 		0.367
(1.00) 		0.0436
(1.00) 		0.363
(1.00) 		0.0173
(1.00) 		0.0252
(1.00)
11p gain 29 (6%) 434 0.11
(1.00) 		0.00121
(0.811) 		0.027
(1.00) 		0.496
(1.00) 		0.00395
(1.00) 		0.0197
(1.00) 		0.369
(1.00) 		0.773
(1.00) 		0.171
(1.00) 		0.63
(1.00)
11q gain 50 (11%) 413 0.615
(1.00) 		0.117
(1.00) 		0.229
(1.00) 		0.0185
(1.00) 		0.0837
(1.00) 		0.141
(1.00) 		0.0614
(1.00) 		0.0726
(1.00) 		0.539
(1.00) 		0.781
(1.00) 		0.32
(1.00) 		0.782
(1.00)
12q gain 15 (3%) 448 0.00771
(1.00) 		0.0386
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.0309
(1.00) 		0.132
(1.00) 		0.0431
(1.00) 		0.029
(1.00) 		0.00385
(1.00) 		0.0284
(1.00)
13q gain 5 (1%) 458 0.0513
(1.00) 		0.136
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.626
(1.00) 		0.719
(1.00) 		0.761
(1.00) 		1
(1.00) 		0.837
(1.00) 		1
(1.00)
14q gain 3 (1%) 460 1
(1.00) 		1
(1.00) 		0.902
(1.00) 		0.416
(1.00) 		0.372
(1.00) 		1
(1.00) 		0.281
(1.00) 		0.608
(1.00)
15q gain 10 (2%) 453 0.0457
(1.00) 		0.0294
(1.00) 		0.114
(1.00) 		0.465
(1.00) 		0.00483
(1.00) 		0.125
(1.00) 		0.0244
(1.00) 		0.556
(1.00) 		0.102
(1.00) 		0.154
(1.00)
16p gain 15 (3%) 448 0.221
(1.00) 		0.485
(1.00) 		0.561
(1.00) 		0.658
(1.00) 		0.0929
(1.00) 		0.138
(1.00) 		0.236
(1.00) 		0.211
(1.00) 		0.0136
(1.00) 		0.00234
(1.00)
16q gain 16 (3%) 447 0.0339
(1.00) 		0.229
(1.00) 		0.469
(1.00) 		0.738
(1.00) 		0.00101
(0.681) 		0.162
(1.00) 		0.679
(1.00) 		0.293
(1.00) 		0.295
(1.00) 		0.00439
(1.00)
17p gain 17 (4%) 446 0.581
(1.00) 		0.505
(1.00) 		0.346
(1.00) 		0.771
(1.00) 		0.000786
(0.538) 		0.28
(1.00) 		0.00139
(0.929) 		0.209
(1.00) 		0.00362
(1.00) 		0.0512
(1.00)
17q gain 19 (4%) 444 0.5
(1.00) 		0.339
(1.00) 		0.346
(1.00) 		0.771
(1.00) 		0.00238
(1.00) 		0.166
(1.00) 		0.00263
(1.00) 		0.0859
(1.00) 		0.0675
(1.00) 		0.0356
(1.00)
21q gain 23 (5%) 440 0.0202
(1.00) 		0.002
(1.00) 		0.11
(1.00) 		0.531
(1.00) 		0.0514
(1.00) 		0.924
(1.00) 		0.252
(1.00) 		0.868
(1.00) 		0.318
(1.00) 		0.727
(1.00)
22q gain 17 (4%) 446 0.109
(1.00) 		0.00082
(0.561) 		1
(1.00) 		0.56
(1.00) 		0.0038
(1.00) 		0.00796
(1.00) 		0.519
(1.00) 		0.48
(1.00) 		0.296
(1.00) 		0.375
(1.00)
1q loss 23 (5%) 440 0.344
(1.00) 		0.144
(1.00) 		0.811
(1.00) 		0.127
(1.00) 		0.552
(1.00) 		0.54
(1.00) 		0.341
(1.00) 		0.304
(1.00) 		0.849
(1.00) 		0.667
(1.00) 		0.336
(1.00) 		0.239
(1.00)
6p loss 28 (6%) 435 0.0377
(1.00) 		0.178
(1.00) 		0.186
(1.00) 		0.708
(1.00) 		0.342
(1.00) 		0.546
(1.00) 		0.869
(1.00) 		0.541
(1.00) 		0.728
(1.00) 		0.453
(1.00)
6q loss 57 (12%) 406 0.000628
(0.433) 		0.00697
(1.00) 		0.254
(1.00) 		0.398
(1.00) 		0.153
(1.00) 		0.0593
(1.00) 		0.254
(1.00) 		0.207
(1.00) 		0.0989
(1.00) 		0.191
(1.00)
7p loss 3 (1%) 460 0.456
(1.00) 		0.332
(1.00) 		0.937
(1.00) 		1
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.943
(1.00) 		1
(1.00)
7q loss 3 (1%) 460 0.0398
(1.00) 		0.332
(1.00) 		0.937
(1.00) 		1
(1.00) 		0.564
(1.00) 		1
(1.00) 		0.351
(1.00) 		1
(1.00)
9q loss 46 (10%) 417 0.393
(1.00) 		0.422
(1.00) 		0.607
(1.00) 		0.506
(1.00) 		0.0258
(1.00) 		0.479
(1.00) 		0.807
(1.00) 		0.695
(1.00) 		0.506
(1.00) 		0.586
(1.00)
12p loss 25 (5%) 438 0.0313
(1.00) 		0.00696
(1.00) 		0.603
(1.00) 		0.51
(1.00) 		0.673
(1.00) 		0.0795
(1.00) 		0.0757
(1.00) 		0.35
(1.00) 		0.107
(1.00) 		0.679
(1.00)
16q loss 20 (4%) 443 0.00377
(1.00) 		0.00249
(1.00) 		0.374
(1.00) 		0.219
(1.00) 		0.0282
(1.00) 		0.396
(1.00) 		0.472
(1.00) 		0.453
(1.00) 		0.556
(1.00) 		0.479
(1.00)
17p loss 14 (3%) 449 0.00468
(1.00) 		0.0945
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.0409
(1.00) 		0.0941
(1.00) 		0.0378
(1.00) 		0.0142
(1.00) 		0.00856
(1.00) 		0.0159
(1.00)
17q loss 9 (2%) 454 0.058
(1.00) 		0.138
(1.00) 		0.835
(1.00) 		0.447
(1.00) 		0.407
(1.00) 		0.227
(1.00) 		0.0579
(1.00) 		0.175
(1.00) 		0.0959
(1.00) 		0.271
(1.00)
18p loss 63 (14%) 400 0.321
(1.00) 		0.316
(1.00) 		0.44
(1.00) 		0.0352
(1.00) 		0.573
(1.00) 		0.0801
(1.00) 		0.561
(1.00) 		0.719
(1.00) 		0.036
(1.00) 		0.222
(1.00) 		0.56
(1.00) 		0.519
(1.00)
18q loss 58 (13%) 405 0.344
(1.00) 		0.212
(1.00) 		0.144
(1.00) 		0.00183
(1.00) 		0.285
(1.00) 		0.202
(1.00) 		0.102
(1.00) 		0.181
(1.00) 		0.559
(1.00) 		0.353
(1.00) 		0.372
(1.00) 		0.615
(1.00)
19p loss 21 (5%) 442 0.847
(1.00) 		0.311
(1.00) 		0.366
(1.00) 		0.757
(1.00) 		0.103
(1.00) 		0.661
(1.00) 		0.00829
(1.00) 		0.113
(1.00) 		0.472
(1.00) 		0.453
(1.00) 		0.76
(1.00) 		0.335
(1.00)
20q loss 3 (1%) 460 0.155
(1.00) 		0.494
(1.00) 		0.00195
(1.00) 		0.293
(1.00) 		0.279
(1.00) 		0.107
(1.00) 		0.111
(1.00) 		0.0173
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 9.4e-05 (Fisher's exact test), Q value = 0.068

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
1P GAIN MUTATED 4 8 0
1P GAIN WILD-TYPE 135 102 214

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 3.28e-05 (Fisher's exact test), Q value = 0.024

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
1P GAIN MUTATED 4 8 0 0
1P GAIN WILD-TYPE 195 57 53 141

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 7.74e-09 (Chi-square test), Q value = 6.1e-06

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
1P GAIN MUTATED 0 10 0 0 2 0
1P GAIN WILD-TYPE 116 79 94 126 9 25

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 3.14e-05 (Chi-square test), Q value = 0.023

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
1P GAIN MUTATED 0 8 3 0 1 0 0
1P GAIN WILD-TYPE 62 68 27 41 135 63 27

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000137 (Chi-square test), Q value = 0.098

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
1P GAIN MUTATED 2 8 0 0 0 2 0
1P GAIN WILD-TYPE 85 69 55 124 39 20 31

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.079

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
1Q GAIN MUTATED 4 12 2
1Q GAIN WILD-TYPE 135 98 212

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.094

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
1Q GAIN MUTATED 6 10 1 1
1Q GAIN WILD-TYPE 193 55 52 140

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.000107 (Chi-square test), Q value = 0.078

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
1Q GAIN MUTATED 1 10 0 4 2 1
1Q GAIN WILD-TYPE 115 79 94 122 9 24

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000353 (Chi-square test), Q value = 0.25

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
1Q GAIN MUTATED 2 8 0 4 0 4 0
1Q GAIN WILD-TYPE 85 69 55 120 39 18 31

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1.67e-06 (Chi-square test), Q value = 0.0013

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
2P GAIN MUTATED 0 4 2 2 3 0
2P GAIN WILD-TYPE 116 85 92 124 8 25

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 2.6e-07 (Chi-square test), Q value = 2e-04

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
2Q GAIN MUTATED 0 4 1 2 3 0
2Q GAIN WILD-TYPE 116 85 93 124 8 25

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.000151 (Chi-square test), Q value = 0.11

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
3Q GAIN MUTATED 0 4 1 1 2 0
3Q GAIN WILD-TYPE 116 85 93 125 9 25

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 5.71e-05 (Chi-square test), Q value = 0.042

Table S13.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
5P GAIN MUTATED 0 5 0 1 2 1
5P GAIN WILD-TYPE 116 84 94 125 9 24

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 7.33e-48 (Fisher's exact test), Q value = 6.1e-45

Table S14.  Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
7P GAIN MUTATED 21 87 9
7P GAIN WILD-TYPE 118 23 205

Figure S14.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 5.97e-24 (Fisher's exact test), Q value = 4.9e-21

Table S15.  Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
7P GAIN MUTATED 38 52 11 14
7P GAIN WILD-TYPE 161 13 42 127

Figure S15.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 8.5e-17 (Chi-square test), Q value = 6.9e-14

Table S16.  Gene #12: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
7P GAIN MUTATED 19 54 8 26 5 3
7P GAIN WILD-TYPE 97 35 86 100 6 22

Figure S16.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.001

Table S17.  Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
7P GAIN MUTATED 78 7 30
7P GAIN WILD-TYPE 146 73 127

Figure S17.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 3.53e-08 (Chi-square test), Q value = 2.7e-05

Table S18.  Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
7P GAIN MUTATED 13 41 9 4 25 15 3
7P GAIN WILD-TYPE 49 35 21 37 111 48 24

Figure S18.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.79e-10 (Chi-square test), Q value = 5.4e-07

Table S19.  Gene #12: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
7P GAIN MUTATED 17 44 6 22 8 7 6
7P GAIN WILD-TYPE 70 33 49 102 31 15 25

Figure S19.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 3.82e-45 (Fisher's exact test), Q value = 3.2e-42

Table S20.  Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
7Q GAIN MUTATED 35 93 17
7Q GAIN WILD-TYPE 104 17 197

Figure S20.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1.92e-19 (Fisher's exact test), Q value = 1.6e-16

Table S21.  Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
7Q GAIN MUTATED 55 53 13 22
7Q GAIN WILD-TYPE 144 12 40 119

Figure S21.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 6.94e-12 (Chi-square test), Q value = 5.6e-09

Table S22.  Gene #13: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
7Q GAIN MUTATED 33 56 11 33 4 6
7Q GAIN WILD-TYPE 83 33 83 93 7 19

Figure S22.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.84e-07 (Fisher's exact test), Q value = 0.00052

Table S23.  Gene #13: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
7Q GAIN MUTATED 92 9 42
7Q GAIN WILD-TYPE 132 71 115

Figure S23.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 2.4e-07 (Chi-square test), Q value = 0.00018

Table S24.  Gene #13: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
7Q GAIN MUTATED 18 44 10 4 33 23 4
7Q GAIN WILD-TYPE 44 32 20 37 103 40 23

Figure S24.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.28e-07 (Chi-square test), Q value = 9.8e-05

Table S25.  Gene #13: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
7Q GAIN MUTATED 23 46 7 31 14 8 7
7Q GAIN WILD-TYPE 64 31 48 93 25 14 24

Figure S25.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0086

Table S26.  Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
8P GAIN MUTATED 24 9 6
8P GAIN WILD-TYPE 115 101 208

Figure S26.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2e-06 (Fisher's exact test), Q value = 0.0015

Table S27.  Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
8Q GAIN MUTATED 29 12 8
8Q GAIN WILD-TYPE 110 98 206

Figure S27.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1.62e-14 (Fisher's exact test), Q value = 1.3e-11

Table S28.  Gene #18: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
10P GAIN MUTATED 39 2 6
10P GAIN WILD-TYPE 100 108 208

Figure S28.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 6.13e-13 (Fisher's exact test), Q value = 4.9e-10

Table S29.  Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
10P GAIN MUTATED 44 1 2 0
10P GAIN WILD-TYPE 155 64 51 141

Figure S29.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 2.34e-09 (Chi-square test), Q value = 1.8e-06

Table S30.  Gene #18: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
10P GAIN MUTATED 23 5 0 10 6 3
10P GAIN WILD-TYPE 93 84 94 116 5 22

Figure S30.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.55e-06 (Fisher's exact test), Q value = 0.0027

Table S31.  Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
10P GAIN MUTATED 37 0 10
10P GAIN WILD-TYPE 187 80 147

Figure S31.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.16

Table S32.  Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
10Q GAIN MUTATED 7 0 0
10Q GAIN WILD-TYPE 132 110 214

Figure S32.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.000291 (Chi-square test), Q value = 0.2

Table S33.  Gene #19: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
10Q GAIN MUTATED 1 1 0 2 2 1
10Q GAIN WILD-TYPE 115 88 94 124 9 24

Figure S33.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.15

Table S34.  Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
12P GAIN MUTATED 17 9 4
12P GAIN WILD-TYPE 122 101 210

Figure S34.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 7.9e-05 (Fisher's exact test), Q value = 0.058

Table S35.  Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
18P GAIN MUTATED 10 5 0
18P GAIN WILD-TYPE 129 105 214

Figure S35.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1.53e-10 (Chi-square test), Q value = 1.2e-07

Table S36.  Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
18P GAIN MUTATED 1 4 0 2 4 3
18P GAIN WILD-TYPE 115 85 94 124 7 22

Figure S36.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 3.48e-08 (Chi-square test), Q value = 2.7e-05

Table S37.  Gene #32: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
18Q GAIN MUTATED 0 5 0 1 3 2
18Q GAIN WILD-TYPE 116 84 94 125 8 23

Figure S37.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1.46e-09 (Fisher's exact test), Q value = 1.2e-06

Table S38.  Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
19P GAIN MUTATED 5 34 50
19P GAIN WILD-TYPE 134 76 164

Figure S38.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 4.97e-16 (Fisher's exact test), Q value = 4e-13

Table S39.  Gene #33: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
19P GAIN MUTATED 9 25 4 49
19P GAIN WILD-TYPE 190 40 49 92

Figure S39.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 3.22e-10 (Chi-square test), Q value = 2.6e-07

Table S40.  Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
19P GAIN MUTATED 4 26 36 22 1 0
19P GAIN WILD-TYPE 112 63 58 104 10 25

Figure S40.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000216 (Fisher's exact test), Q value = 0.15

Table S41.  Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
19P GAIN MUTATED 32 29 28
19P GAIN WILD-TYPE 192 51 129

Figure S41.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 8.46e-05 (Chi-square test), Q value = 0.062

Table S42.  Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
19P GAIN MUTATED 4 20 4 18 25 11 2
19P GAIN WILD-TYPE 58 56 26 23 111 52 25

Figure S42.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.8e-07 (Chi-square test), Q value = 0.00044

Table S43.  Gene #33: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
19P GAIN MUTATED 4 23 23 22 7 3 2
19P GAIN WILD-TYPE 83 54 32 102 32 19 29

Figure S43.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 6.12e-14 (Fisher's exact test), Q value = 4.9e-11

Table S44.  Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
19Q GAIN MUTATED 0 23 1
19Q GAIN WILD-TYPE 139 87 213

Figure S44.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 3.92e-15 (Fisher's exact test), Q value = 3.2e-12

Table S45.  Gene #34: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
19Q GAIN MUTATED 1 20 2 0
19Q GAIN WILD-TYPE 198 45 51 141

Figure S45.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 7.94e-12 (Chi-square test), Q value = 6.3e-09

Table S46.  Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
19Q GAIN MUTATED 0 19 0 5 0 0
19Q GAIN WILD-TYPE 116 70 94 121 11 25

Figure S46.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.17

Table S47.  Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
19Q GAIN MUTATED 21 0 3
19Q GAIN WILD-TYPE 203 80 154

Figure S47.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 3.68e-09 (Chi-square test), Q value = 2.9e-06

Table S48.  Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
19Q GAIN MUTATED 0 16 0 0 4 1 1
19Q GAIN WILD-TYPE 62 60 30 41 132 62 26

Figure S48.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.72e-11 (Chi-square test), Q value = 7.7e-08

Table S49.  Gene #34: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
19Q GAIN MUTATED 0 17 0 4 0 0 1
19Q GAIN WILD-TYPE 87 60 55 120 39 22 30

Figure S49.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 5.97e-12 (Fisher's exact test), Q value = 4.8e-09

Table S50.  Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
20P GAIN MUTATED 8 30 4
20P GAIN WILD-TYPE 131 80 210

Figure S50.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 3.45e-13 (Fisher's exact test), Q value = 2.8e-10

Table S51.  Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
20P GAIN MUTATED 7 26 4 5
20P GAIN WILD-TYPE 192 39 49 136

Figure S51.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 7.62e-08 (Chi-square test), Q value = 5.9e-05

Table S52.  Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
20P GAIN MUTATED 4 23 4 9 2 0
20P GAIN WILD-TYPE 112 66 90 117 9 25

Figure S52.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 2.61e-06 (Chi-square test), Q value = 0.002

Table S53.  Gene #35: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
20P GAIN MUTATED 0 18 4 2 6 9 0
20P GAIN WILD-TYPE 62 58 26 39 130 54 27

Figure S53.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.74e-10 (Chi-square test), Q value = 1.4e-07

Table S54.  Gene #35: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
20P GAIN MUTATED 0 23 2 7 4 3 0
20P GAIN WILD-TYPE 87 54 53 117 35 19 31

Figure S54.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 5.97e-12 (Fisher's exact test), Q value = 4.8e-09

Table S55.  Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
20Q GAIN MUTATED 8 30 4
20Q GAIN WILD-TYPE 131 80 210

Figure S55.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5.69e-14 (Fisher's exact test), Q value = 4.6e-11

Table S56.  Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
20Q GAIN MUTATED 8 27 2 5
20Q GAIN WILD-TYPE 191 38 51 136

Figure S56.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 7.14e-10 (Chi-square test), Q value = 5.6e-07

Table S57.  Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
20Q GAIN MUTATED 4 25 4 7 2 0
20Q GAIN WILD-TYPE 112 64 90 119 9 25

Figure S57.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 6.28e-08 (Chi-square test), Q value = 4.9e-05

Table S58.  Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
20Q GAIN MUTATED 1 20 3 2 4 10 0
20Q GAIN WILD-TYPE 61 56 27 39 132 53 27

Figure S58.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.19e-12 (Chi-square test), Q value = 1.8e-09

Table S59.  Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
20Q GAIN MUTATED 1 25 2 5 5 2 0
20Q GAIN WILD-TYPE 86 52 53 119 34 20 31

Figure S59.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1.79e-08 (Fisher's exact test), Q value = 1.4e-05

Table S60.  Gene #39: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
XQ GAIN MUTATED 26 6 3
XQ GAIN WILD-TYPE 113 104 211

Figure S60.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 8.22e-07 (Fisher's exact test), Q value = 0.00062

Table S61.  Gene #39: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
XQ GAIN MUTATED 29 3 3 0
XQ GAIN WILD-TYPE 170 62 50 141

Figure S61.  Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.12

Table S62.  Gene #40: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 6 10 4
1P LOSS MUTATED 7 2 1 0
1P LOSS WILD-TYPE 0 4 9 4

Figure S62.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 6.36e-47 (Fisher's exact test), Q value = 5.3e-44

Table S63.  Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
1P LOSS MUTATED 6 13 149
1P LOSS WILD-TYPE 133 97 65

Figure S63.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 4.6e-95 (Fisher's exact test), Q value = 3.9e-92

Table S64.  Gene #40: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
1P LOSS MUTATED 5 4 16 140
1P LOSS WILD-TYPE 194 61 37 1

Figure S64.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.22

Table S65.  Gene #40: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
1P LOSS MUTATED 8 15 26 36
1P LOSS WILD-TYPE 44 47 42 38

Figure S65.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 9.13e-52 (Chi-square test), Q value = 7.6e-49

Table S66.  Gene #40: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
1P LOSS MUTATED 3 7 92 56 1 9
1P LOSS WILD-TYPE 113 82 2 70 10 16

Figure S66.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.06e-65 (Fisher's exact test), Q value = 7.6e-62

Table S67.  Gene #40: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
1P LOSS MUTATED 11 80 77
1P LOSS WILD-TYPE 213 0 80

Figure S67.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1.7e-22 (Chi-square test), Q value = 1.4e-19

Table S68.  Gene #40: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
1P LOSS MUTATED 4 12 2 37 65 21 16
1P LOSS WILD-TYPE 58 64 28 4 71 42 11

Figure S68.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0016

Table S69.  Gene #40: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 16 225
1P LOSS MUTATED 95 5 57
1P LOSS WILD-TYPE 99 11 168

Figure S69.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.07e-27 (Chi-square test), Q value = 5.8e-24

Table S70.  Gene #40: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
1P LOSS MUTATED 4 14 49 61 13 1 15
1P LOSS WILD-TYPE 83 63 6 63 26 21 16

Figure S70.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.089

Table S71.  Gene #40: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 196 234
1P LOSS MUTATED 1 91 65
1P LOSS WILD-TYPE 4 105 169

Figure S71.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.025

Table S72.  Gene #42: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
2P LOSS MUTATED 15 1 3
2P LOSS WILD-TYPE 124 109 211

Figure S72.  Get High-res Image Gene #42: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 5.82e-06 (Fisher's exact test), Q value = 0.0044

Table S73.  Gene #43: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
2Q LOSS MUTATED 15 0 3
2Q LOSS WILD-TYPE 124 110 211

Figure S73.  Get High-res Image Gene #43: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 8.6e-05 (Chi-square test), Q value = 0.063

Table S74.  Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
3P LOSS MUTATED 6 8 2 4 4 1
3P LOSS WILD-TYPE 110 81 92 122 7 24

Figure S74.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Chi-square test), Q value = 0.14

Table S75.  Gene #45: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
3Q LOSS MUTATED 6 7 2 5 4 1
3Q LOSS WILD-TYPE 110 82 92 121 7 24

Figure S75.  Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 4.77e-10 (Fisher's exact test), Q value = 3.8e-07

Table S76.  Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
4P LOSS MUTATED 22 1 1 43
4P LOSS WILD-TYPE 177 64 52 98

Figure S76.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 3.54e-08 (Chi-square test), Q value = 2.7e-05

Table S77.  Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
4P LOSS MUTATED 12 1 30 17 4 2
4P LOSS WILD-TYPE 104 88 64 109 7 23

Figure S77.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.94e-07 (Fisher's exact test), Q value = 0.00045

Table S78.  Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
4P LOSS MUTATED 15 25 26
4P LOSS WILD-TYPE 209 55 131

Figure S78.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'METHLYATION_CNMF'

P value = 8.29e-09 (Fisher's exact test), Q value = 6.5e-06

Table S79.  Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
4Q LOSS MUTATED 35 1 3 46
4Q LOSS WILD-TYPE 164 64 50 95

Figure S79.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1.27e-07 (Chi-square test), Q value = 9.8e-05

Table S80.  Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
4Q LOSS MUTATED 17 3 32 23 6 3
4Q LOSS WILD-TYPE 99 86 62 103 5 22

Figure S80.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.23e-05 (Fisher's exact test), Q value = 0.06

Table S81.  Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
4Q LOSS MUTATED 26 27 31
4Q LOSS WILD-TYPE 198 53 126

Figure S81.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 3.68e-06 (Fisher's exact test), Q value = 0.0028

Table S82.  Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
5P LOSS MUTATED 22 6 4
5P LOSS WILD-TYPE 117 104 210

Figure S82.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 8.78e-07 (Fisher's exact test), Q value = 0.00067

Table S83.  Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
5Q LOSS MUTATED 22 3 4
5Q LOSS WILD-TYPE 117 107 210

Figure S83.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1.67e-07 (Chi-square test), Q value = 0.00013

Table S84.  Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
5Q LOSS MUTATED 8 9 2 2 5 2
5Q LOSS WILD-TYPE 108 80 92 124 6 23

Figure S84.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.16

Table S85.  Gene #49: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 196 234
5Q LOSS MUTATED 3 6 19
5Q LOSS WILD-TYPE 2 190 215

Figure S85.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.011

Table S86.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
8P LOSS MUTATED 7 10 0
8P LOSS WILD-TYPE 132 100 214

Figure S86.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 9.6e-05 (Fisher's exact test), Q value = 0.07

Table S87.  Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
8P LOSS MUTATED 7 9 1 0
8P LOSS WILD-TYPE 192 56 52 141

Figure S87.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 2.08e-07 (Chi-square test), Q value = 0.00016

Table S88.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
8P LOSS MUTATED 1 10 0 2 3 1
8P LOSS WILD-TYPE 115 79 94 124 8 24

Figure S88.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 2.93e-05 (Chi-square test), Q value = 0.022

Table S89.  Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
8P LOSS MUTATED 0 11 2 1 3 0 0
8P LOSS WILD-TYPE 62 65 28 40 133 63 27

Figure S89.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.32e-05 (Chi-square test), Q value = 0.017

Table S90.  Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
8P LOSS MUTATED 0 11 1 2 0 2 1
8P LOSS WILD-TYPE 87 66 54 122 39 20 30

Figure S90.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.1

Table S91.  Gene #55: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
8Q LOSS MUTATED 3 8 0
8Q LOSS WILD-TYPE 136 102 214

Figure S91.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.012

Table S92.  Gene #55: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
8Q LOSS MUTATED 2 8 1 0
8Q LOSS WILD-TYPE 197 57 52 141

Figure S92.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.000108 (Chi-square test), Q value = 0.078

Table S93.  Gene #55: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
8Q LOSS MUTATED 0 8 0 1 1 1
8Q LOSS WILD-TYPE 116 81 94 125 10 24

Figure S93.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.000285 (Chi-square test), Q value = 0.2

Table S94.  Gene #55: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
8Q LOSS MUTATED 0 8 1 0 2 0 0
8Q LOSS WILD-TYPE 62 68 29 41 134 63 27

Figure S94.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000231 (Chi-square test), Q value = 0.16

Table S95.  Gene #55: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
8Q LOSS MUTATED 0 8 0 1 0 1 1
8Q LOSS WILD-TYPE 87 69 55 123 39 21 30

Figure S95.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 4.22e-06 (Fisher's exact test), Q value = 0.0032

Table S96.  Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
9P LOSS MUTATED 40 39 28
9P LOSS WILD-TYPE 99 71 186

Figure S96.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.000274 (Fisher's exact test), Q value = 0.19

Table S97.  Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
9P LOSS MUTATED 56 23 7 19
9P LOSS WILD-TYPE 143 42 46 122

Figure S97.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 4.58e-40 (Fisher's exact test), Q value = 3.8e-37

Table S98.  Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
10P LOSS MUTATED 4 67 5
10P LOSS WILD-TYPE 135 43 209

Figure S98.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 2.75e-49 (Fisher's exact test), Q value = 2.3e-46

Table S99.  Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
10P LOSS MUTATED 3 57 9 6
10P LOSS WILD-TYPE 196 8 44 135

Figure S99.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 2.54e-07 (Fisher's exact test), Q value = 0.00019

Table S100.  Gene #58: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
10P LOSS MUTATED 4 24 3 6
10P LOSS WILD-TYPE 48 38 65 68

Figure S100.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 2.15e-37 (Chi-square test), Q value = 1.8e-34

Table S101.  Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
10P LOSS MUTATED 1 56 2 14 1 1
10P LOSS WILD-TYPE 115 33 92 112 10 24

Figure S101.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-08 (Fisher's exact test), Q value = 8.6e-06

Table S102.  Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
10P LOSS MUTATED 59 2 14
10P LOSS WILD-TYPE 165 78 143

Figure S102.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1.58e-15 (Chi-square test), Q value = 1.3e-12

Table S103.  Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
10P LOSS MUTATED 1 38 4 1 15 12 2
10P LOSS WILD-TYPE 61 38 26 40 121 51 25

Figure S103.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.8e-05 (Fisher's exact test), Q value = 0.021

Table S104.  Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 16 225
10P LOSS MUTATED 16 2 55
10P LOSS WILD-TYPE 178 14 170

Figure S104.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.13e-28 (Chi-square test), Q value = 9.3e-26

Table S105.  Gene #58: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
10P LOSS MUTATED 1 48 2 12 4 1 5
10P LOSS WILD-TYPE 86 29 53 112 35 21 26

Figure S105.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.47e-33 (Fisher's exact test), Q value = 1.2e-30

Table S106.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
10Q LOSS MUTATED 16 68 7
10Q LOSS WILD-TYPE 123 42 207

Figure S106.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 2.75e-40 (Fisher's exact test), Q value = 2.3e-37

Table S107.  Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
10Q LOSS MUTATED 17 57 10 6
10Q LOSS WILD-TYPE 182 8 43 135

Figure S107.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.001

Table S108.  Gene #59: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
10Q LOSS MUTATED 6 27 7 7
10Q LOSS WILD-TYPE 46 35 61 67

Figure S108.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2.76e-35 (Chi-square test), Q value = 2.3e-32

Table S109.  Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
10Q LOSS MUTATED 6 60 2 17 4 1
10Q LOSS WILD-TYPE 110 29 92 109 7 24

Figure S109.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.69e-11 (Fisher's exact test), Q value = 3.7e-08

Table S110.  Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
10Q LOSS MUTATED 71 2 17
10Q LOSS WILD-TYPE 153 78 140

Figure S110.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 2.76e-16 (Chi-square test), Q value = 2.3e-13

Table S111.  Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
10Q LOSS MUTATED 1 42 7 2 18 15 2
10Q LOSS WILD-TYPE 61 34 23 39 118 48 25

Figure S111.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.17e-06 (Fisher's exact test), Q value = 0.0031

Table S112.  Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 16 225
10Q LOSS MUTATED 19 4 64
10Q LOSS WILD-TYPE 175 12 161

Figure S112.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.19e-25 (Chi-square test), Q value = 9.8e-23

Table S113.  Gene #59: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
10Q LOSS MUTATED 3 51 4 14 7 3 5
10Q LOSS WILD-TYPE 84 26 51 110 32 19 26

Figure S113.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 5.02e-14 (Fisher's exact test), Q value = 4.1e-11

Table S114.  Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
11P LOSS MUTATED 41 11 4
11P LOSS WILD-TYPE 98 99 210

Figure S114.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1.23e-10 (Fisher's exact test), Q value = 9.8e-08

Table S115.  Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
11P LOSS MUTATED 42 11 3 0
11P LOSS WILD-TYPE 157 54 50 141

Figure S115.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 5.15e-12 (Chi-square test), Q value = 4.1e-09

Table S116.  Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
11P LOSS MUTATED 11 21 0 9 7 7
11P LOSS WILD-TYPE 105 68 94 117 4 18

Figure S116.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.73e-09 (Fisher's exact test), Q value = 6.8e-06

Table S117.  Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
11P LOSS MUTATED 46 0 9
11P LOSS WILD-TYPE 178 80 148

Figure S117.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.14

Table S118.  Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
11Q LOSS MUTATED 9 9 1
11Q LOSS WILD-TYPE 130 101 213

Figure S118.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.11

Table S119.  Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
11Q LOSS MUTATED 8 9 2 0
11Q LOSS WILD-TYPE 191 56 51 141

Figure S119.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 8.75e-08 (Chi-square test), Q value = 6.8e-05

Table S120.  Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
11Q LOSS MUTATED 0 11 0 3 3 2
11Q LOSS WILD-TYPE 116 78 94 123 8 23

Figure S120.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 2.11e-08 (Fisher's exact test), Q value = 1.6e-05

Table S121.  Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
12Q LOSS MUTATED 32 2 13
12Q LOSS WILD-TYPE 107 108 201

Figure S121.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 2.36e-07 (Fisher's exact test), Q value = 0.00018

Table S122.  Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
12Q LOSS MUTATED 38 0 4 5
12Q LOSS WILD-TYPE 161 65 49 136

Figure S122.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 3.5e-08 (Fisher's exact test), Q value = 2.7e-05

Table S123.  Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
13Q LOSS MUTATED 55 22 27
13Q LOSS WILD-TYPE 84 88 187

Figure S123.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.000151 (Fisher's exact test), Q value = 0.11

Table S124.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
14Q LOSS MUTATED 24 23 6 16
14Q LOSS WILD-TYPE 175 42 47 125

Figure S124.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 5.7e-05 (Chi-square test), Q value = 0.042

Table S125.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
14Q LOSS MUTATED 9 28 9 16 2 5
14Q LOSS WILD-TYPE 107 61 85 110 9 20

Figure S125.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000104 (Chi-square test), Q value = 0.075

Table S126.  Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
14Q LOSS MUTATED 9 27 5 15 5 2 6
14Q LOSS WILD-TYPE 78 50 50 109 34 20 25

Figure S126.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.000104 (Chi-square test), Q value = 0.076

Table S127.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
15Q LOSS MUTATED 4 9 21 7 2 2
15Q LOSS WILD-TYPE 112 80 73 119 9 23

Figure S127.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 4.53e-05 (Chi-square test), Q value = 0.033

Table S128.  Gene #67: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
16P LOSS MUTATED 1 4 2 3 3 0
16P LOSS WILD-TYPE 115 85 92 123 8 25

Figure S128.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1.11e-35 (Fisher's exact test), Q value = 9.2e-33

Table S129.  Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
19Q LOSS MUTATED 21 16 153
19Q LOSS WILD-TYPE 118 94 61

Figure S129.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1.07e-75 (Fisher's exact test), Q value = 9e-73

Table S130.  Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
19Q LOSS MUTATED 27 4 16 140
19Q LOSS WILD-TYPE 172 61 37 1

Figure S130.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 6.85e-42 (Chi-square test), Q value = 5.7e-39

Table S131.  Gene #74: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
19Q LOSS MUTATED 14 9 92 59 4 11
19Q LOSS WILD-TYPE 102 80 2 67 7 14

Figure S131.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.33e-49 (Fisher's exact test), Q value = 1.1e-46

Table S132.  Gene #74: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
19Q LOSS MUTATED 28 79 82
19Q LOSS WILD-TYPE 196 1 75

Figure S132.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1.83e-16 (Chi-square test), Q value = 1.5e-13

Table S133.  Gene #74: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 62 76 30 41 136 63 27
19Q LOSS MUTATED 10 15 7 37 71 23 16
19Q LOSS WILD-TYPE 52 61 23 4 65 40 11

Figure S133.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.94e-06 (Fisher's exact test), Q value = 0.0059

Table S134.  Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 16 225
19Q LOSS MUTATED 104 6 69
19Q LOSS WILD-TYPE 90 10 156

Figure S134.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-20 (Chi-square test), Q value = 2.5e-17

Table S135.  Gene #74: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 87 77 55 124 39 22 31
19Q LOSS MUTATED 13 14 49 65 15 6 17
19Q LOSS WILD-TYPE 74 63 6 59 24 16 14

Figure S135.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000259 (Fisher's exact test), Q value = 0.18

Table S136.  Gene #74: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 196 234
19Q LOSS MUTATED 0 99 80
19Q LOSS WILD-TYPE 5 97 154

Figure S136.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 1.05e-06 (Chi-square test), Q value = 8e-04

Table S137.  Gene #75: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
20P LOSS MUTATED 2 0 0 0 2 1
20P LOSS WILD-TYPE 114 89 94 126 9 24

Figure S137.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.11

Table S138.  Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
21Q LOSS MUTATED 21 5 7
21Q LOSS WILD-TYPE 118 105 207

Figure S138.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 7.69e-12 (Fisher's exact test), Q value = 6.2e-09

Table S139.  Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 110 214
22Q LOSS MUTATED 23 25 2
22Q LOSS WILD-TYPE 116 85 212

Figure S139.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.04e-07 (Fisher's exact test), Q value = 8e-05

Table S140.  Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 65 53 141
22Q LOSS MUTATED 20 20 7 3
22Q LOSS WILD-TYPE 179 45 46 138

Figure S140.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 7.58e-05 (Fisher's exact test), Q value = 0.056

Table S141.  Gene #78: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
22Q LOSS MUTATED 2 18 5 4
22Q LOSS WILD-TYPE 50 44 63 70

Figure S141.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 2.02e-07 (Chi-square test), Q value = 0.00016

Table S142.  Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
22Q LOSS MUTATED 8 23 2 10 4 2
22Q LOSS WILD-TYPE 108 66 92 116 7 23

Figure S142.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000187 (Fisher's exact test), Q value = 0.13

Table S143.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
22Q LOSS MUTATED 37 2 10
22Q LOSS WILD-TYPE 187 78 147

Figure S143.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1.05e-05 (Chi-square test), Q value = 0.0078

Table S144.  Gene #79: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 89 94 126 11 25
XQ LOSS MUTATED 9 13 23 10 5 0
XQ LOSS WILD-TYPE 107 76 71 116 6 25

Figure S144.  Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000162 (Fisher's exact test), Q value = 0.12

Table S145.  Gene #79: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 80 157
XQ LOSS MUTATED 29 21 10
XQ LOSS WILD-TYPE 195 59 147

Figure S145.  Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtypes file = LGG-TP.transferedmergedcluster.txt

  • Number of patients = 463

  • Number of significantly arm-level cnvs = 79

  • Number of molecular subtypes = 12

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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