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

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

Summary

Testing the association between copy number variation 40 focal events and 12 molecular subtypes across 365 patients, 96 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 2p cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 2q cnv correlated to 'MRNASEQ_CNMF'.

  • 3p cnv correlated to 'MRNASEQ_CNMF'.

  • 3q cnv correlated to 'MRNASEQ_CNMF'.

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

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

  • 5p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 5q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6q cnv correlated to 'CN_CNMF'.

  • 7p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 8p cnv correlated to 'CN_CNMF'.

  • 8q cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p cnv correlated to 'MRNASEQ_CNMF'.

  • 9q cnv correlated to 'MRNASEQ_CNMF'.

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

  • 10q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q cnv correlated to 'CN_CNMF'.

  • 13q cnv correlated to 'MRNA_CHIERARCHICAL'.

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

  • 15q cnv correlated to 'MRNASEQ_CNMF'.

  • 16p cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 17p cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 17q cnv correlated to 'MRNASEQ_CNMF'.

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

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

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

  • 20q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 focal 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, 96 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 142 (39%) 223 0.00608
(1.00) 		0.00067
(0.25) 		2.66e-47
(1.24e-44) 		1.49e-64
(6.98e-62) 		0.00257
(0.886) 		0.189
(1.00) 		2.91e-33
(1.35e-30) 		2.57e-37
(1.19e-34) 		7.46e-08
(3.26e-05) 		9.26e-05
(0.0373) 		8.35e-09
(3.7e-06) 		3.42e-07
(0.000147)
10p 93 (25%) 272 0.446
(1.00) 		0.042
(1.00) 		2.33e-18
(1.06e-15) 		2.69e-26
(1.23e-23) 		2.03e-05
(0.00837) 		0.00248
(0.858) 		2.51e-16
(1.13e-13) 		8.14e-11
(3.65e-08) 		0.000657
(0.246) 		0.0102
(1.00) 		1.31e-07
(5.66e-05) 		2.56e-07
(0.000111)
10q 74 (20%) 291 0.0838
(1.00) 		0.164
(1.00) 		6.69e-24
(3.05e-21) 		3.17e-30
(1.46e-27) 		2e-06
(0.000849) 		0.000399
(0.153) 		4.77e-23
(2.17e-20) 		1.13e-07
(4.9e-05) 		0.0222
(1.00) 		0.1
(1.00) 		2.36e-11
(1.06e-08) 		1.67e-05
(0.00691)
19q 166 (45%) 199 0.132
(1.00) 		0.159
(1.00) 		6.79e-42
(3.16e-39) 		1.16e-50
(5.4e-48) 		0.0714
(1.00) 		0.415
(1.00) 		1.42e-25
(6.48e-23) 		3.25e-29
(1.5e-26) 		0.000207
(0.0822) 		0.000572
(0.215) 		2.58e-07
(0.000111) 		4.22e-05
(0.0173)
7p 91 (25%) 274 0.745
(1.00) 		0.648
(1.00) 		4.4e-28
(2.02e-25) 		2.31e-15
(1.04e-12) 		0.00039
(0.15) 		0.0101
(1.00) 		2.8e-12
(1.26e-09) 		7.45e-06
(0.00311) 		0.00136
(0.49) 		0.0157
(1.00) 		1.29e-05
(0.00535) 		6.9e-07
(0.000296)
7q 116 (32%) 249 0.764
(1.00) 		0.495
(1.00) 		2.04e-28
(9.41e-26) 		5.95e-14
(2.69e-11) 		0.00512
(1.00) 		0.0288
(1.00) 		2.31e-08
(1.02e-05) 		4.08e-06
(0.00171) 		0.00595
(1.00) 		0.0508
(1.00) 		0.000523
(0.197) 		4.27e-05
(0.0175)
20q 35 (10%) 330 7.58e-08
(3.3e-05) 		1.03e-10
(4.61e-08) 		0.000898
(0.33) 		0.11
(1.00) 		7.85e-09
(3.48e-06) 		5.17e-05
(0.021) 		0.0117
(1.00) 		0.0302
(1.00) 		4.62e-05
(0.0189) 		0.000242
(0.0953)
4q 73 (20%) 292 1
(1.00) 		0.196
(1.00) 		0.00399
(1.00) 		3.84e-06
(0.00162) 		0.196
(1.00) 		0.0934
(1.00) 		2.56e-06
(0.00108) 		4.08e-06
(0.00171) 		0.00865
(1.00) 		0.000777
(0.287) 		0.000436
(0.166) 		0.0695
(1.00)
5q 31 (8%) 334 0.446
(1.00) 		0.0182
(1.00) 		0.000123
(0.0493) 		0.000257
(0.1) 		0.0109
(1.00) 		0.38
(1.00) 		2.7e-10
(1.2e-07) 		0.000326
(0.126) 		0.00878
(1.00) 		0.00238
(0.828) 		0.00289
(0.993) 		0.0418
(1.00)
4p 62 (17%) 303 0.864
(1.00) 		0.648
(1.00) 		0.00198
(0.7) 		9.89e-07
(0.000422) 		0.502
(1.00) 		0.0742
(1.00) 		7.15e-07
(0.000306) 		1.32e-05
(0.00548) 		0.0658
(1.00) 		0.00412
(1.00) 		0.00102
(0.371) 		0.333
(1.00)
5p 34 (9%) 331 0.873
(1.00) 		0.00344
(1.00) 		2.02e-06
(0.000858) 		5.21e-05
(0.0211) 		0.424
(1.00) 		1
(1.00) 		4.64e-05
(0.0189) 		0.00224
(0.788) 		0.0505
(1.00) 		0.0125
(1.00) 		0.016
(1.00) 		0.448
(1.00)
8q 45 (12%) 320 0.446
(1.00) 		0.0182
(1.00) 		1.51e-05
(0.00627) 		0.00181
(0.641) 		0.0111
(1.00) 		0.59
(1.00) 		0.00757
(1.00) 		0.000286
(0.111) 		0.0545
(1.00) 		0.0288
(1.00) 		0.0277
(1.00) 		0.00039
(0.15)
14q 59 (16%) 306 0.467
(1.00) 		0.473
(1.00) 		0.000232
(0.0915) 		0.00228
(0.796) 		0.061
(1.00) 		0.163
(1.00) 		0.000195
(0.0778) 		0.0744
(1.00) 		0.00102
(0.371) 		0.00451
(1.00) 		0.000426
(0.162) 		0.0753
(1.00)
19p 82 (22%) 283 0.113
(1.00) 		0.135
(1.00) 		2.72e-05
(0.0112) 		3.12e-08
(1.37e-05) 		0.181
(1.00) 		0.265
(1.00) 		0.00051
(0.193) 		0.0114
(1.00) 		0.269
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.79
(1.00)
20p 37 (10%) 328 0.271
(1.00) 		0.0879
(1.00) 		1.5e-08
(6.63e-06) 		6.54e-09
(2.91e-06) 		0.000988
(0.361) 		0.126
(1.00) 		2.13e-06
(0.000901) 		0.000815
(0.301) 		0.187
(1.00) 		0.133
(1.00) 		0.00215
(0.755) 		0.00173
(0.616)
16p 22 (6%) 343 0.271
(1.00) 		0.0325
(1.00) 		0.0947
(1.00) 		0.248
(1.00) 		0.494
(1.00) 		0.853
(1.00) 		1.61e-06
(0.000687) 		0.626
(1.00) 		0.0996
(1.00) 		0.000297
(0.115) 		0.387
(1.00) 		0.00439
(1.00)
17p 24 (7%) 341 0.0321
(1.00) 		0.231
(1.00) 		0.565
(1.00) 		0.853
(1.00) 		7.48e-08
(3.26e-05) 		0.0276
(1.00) 		0.00524
(1.00) 		0.000222
(0.0875) 		0.00111
(0.402) 		0.00535
(1.00)
22q 51 (14%) 314 0.815
(1.00) 		0.106
(1.00) 		0.00336
(1.00) 		0.0164
(1.00) 		0.000195
(0.0778) 		0.0166
(1.00) 		0.000215
(0.085) 		0.0693
(1.00) 		0.225
(1.00) 		0.365
(1.00) 		0.00856
(1.00) 		0.163
(1.00)
2p 22 (6%) 343 0.754
(1.00) 		0.749
(1.00) 		0.0947
(1.00) 		0.191
(1.00) 		0.134
(1.00) 		0.696
(1.00) 		0.000762
(0.283) 		0.0415
(1.00) 		0.0998
(1.00) 		0.000154
(0.0618) 		0.119
(1.00) 		0.03
(1.00)
2q 20 (5%) 345 1
(1.00) 		0.212
(1.00) 		0.16
(1.00) 		0.0987
(1.00) 		0.0203
(1.00) 		1
(1.00) 		0.000267
(0.104) 		0.0488
(1.00) 		0.0678
(1.00) 		0.02
(1.00) 		0.0544
(1.00) 		0.0137
(1.00)
3p 27 (7%) 338 0.343
(1.00) 		0.645
(1.00) 		0.00793
(1.00) 		0.225
(1.00) 		8.38e-09
(3.71e-06) 		0.0565
(1.00) 		0.0514
(1.00) 		0.0257
(1.00) 		0.0922
(1.00) 		0.0235
(1.00)
3q 29 (8%) 336 0.651
(1.00) 		0.164
(1.00) 		0.238
(1.00) 		0.593
(1.00) 		0.044
(1.00) 		0.11
(1.00) 		6.32e-08
(2.77e-05) 		0.0624
(1.00) 		0.088
(1.00) 		0.0654
(1.00) 		0.158
(1.00) 		0.0383
(1.00)
6q 51 (14%) 314 0.000247
(0.097) 		0.00158
(0.566) 		0.159
(1.00) 		0.431
(1.00) 		0.109
(1.00) 		0.0313
(1.00) 		0.00177
(0.63) 		0.266
(1.00) 		0.175
(1.00) 		0.00745
(1.00)
8p 42 (12%) 323 0.839
(1.00) 		0.022
(1.00) 		5.53e-05
(0.0223) 		0.00225
(0.788) 		0.0483
(1.00) 		0.604
(1.00) 		0.0128
(1.00) 		0.0012
(0.435) 		0.0981
(1.00) 		0.0416
(1.00) 		0.0118
(1.00) 		0.00143
(0.514)
9p 95 (26%) 270 0.745
(1.00) 		0.648
(1.00) 		0.00165
(0.587) 		0.000977
(0.357) 		0.00591
(1.00) 		0.0449
(1.00) 		0.000494
(0.187) 		0.187
(1.00) 		0.813
(1.00) 		0.126
(1.00) 		0.162
(1.00) 		0.0558
(1.00)
9q 51 (14%) 314 1
(1.00) 		0.212
(1.00) 		0.209
(1.00) 		0.622
(1.00) 		0.135
(1.00) 		0.59
(1.00) 		0.000401
(0.153) 		0.611
(1.00) 		0.846
(1.00) 		0.0282
(1.00) 		0.137
(1.00) 		0.779
(1.00)
12q 46 (13%) 319 1
(1.00) 		0.00815
(1.00) 		8.12e-06
(0.00339) 		0.00497
(1.00) 		1
(1.00) 		0.912
(1.00) 		0.192
(1.00) 		0.000871
(0.321) 		0.271
(1.00) 		0.145
(1.00) 		0.078
(1.00) 		0.493
(1.00)
13q 89 (24%) 276 0.18
(1.00) 		0.000618
(0.232) 		0.0501
(1.00) 		0.0119
(1.00) 		0.0284
(1.00) 		0.517
(1.00) 		0.0485
(1.00) 		0.205
(1.00) 		0.214
(1.00) 		0.0531
(1.00) 		0.0531
(1.00) 		0.174
(1.00)
15q 40 (11%) 325 0.574
(1.00) 		0.404
(1.00) 		0.121
(1.00) 		0.00772
(1.00) 		0.0471
(1.00) 		0.0174
(1.00) 		0.000272
(0.106) 		0.0237
(1.00) 		0.04
(1.00) 		0.0568
(1.00) 		0.49
(1.00) 		0.0601
(1.00)
17q 21 (6%) 344 0.201
(1.00) 		0.664
(1.00) 		0.785
(1.00) 		0.708
(1.00) 		0.000163
(0.0652) 		0.189
(1.00) 		0.00595
(1.00) 		0.0127
(1.00) 		0.00313
(1.00) 		0.00338
(1.00)
1q 33 (9%) 332 0.0942
(1.00) 		0.212
(1.00) 		0.0352
(1.00) 		0.0758
(1.00) 		0.188
(1.00) 		0.652
(1.00) 		0.00529
(1.00) 		0.916
(1.00) 		0.393
(1.00) 		0.0155
(1.00) 		0.385
(1.00) 		0.447
(1.00)
6p 29 (8%) 336 0.118
(1.00) 		0.101
(1.00) 		0.0585
(1.00) 		0.683
(1.00) 		0.0932
(1.00) 		0.173
(1.00) 		0.0526
(1.00) 		0.511
(1.00) 		0.433
(1.00) 		0.000751
(0.279)
11p 71 (19%) 294 0.552
(1.00) 		0.068
(1.00) 		0.0305
(1.00) 		0.0119
(1.00) 		0.249
(1.00) 		0.25
(1.00) 		0.00349
(1.00) 		0.244
(1.00) 		0.223
(1.00) 		0.0499
(1.00) 		0.194
(1.00) 		0.19
(1.00)
11q 59 (16%) 306 0.0708
(1.00) 		0.00315
(1.00) 		0.87
(1.00) 		0.588
(1.00) 		0.689
(1.00) 		0.139
(1.00) 		0.03
(1.00) 		0.72
(1.00) 		0.908
(1.00) 		0.0349
(1.00) 		0.819
(1.00) 		0.35
(1.00)
12p 42 (12%) 323 0.508
(1.00) 		0.106
(1.00) 		0.00242
(0.839) 		0.0367
(1.00) 		0.366
(1.00) 		0.843
(1.00) 		0.301
(1.00) 		0.00735
(1.00) 		0.0435
(1.00) 		0.00381
(1.00) 		0.0143
(1.00) 		0.0818
(1.00)
16q 29 (8%) 336 0.651
(1.00) 		0.164
(1.00) 		0.036
(1.00) 		0.0167
(1.00) 		0.426
(1.00) 		0.528
(1.00) 		0.00824
(1.00) 		0.294
(1.00) 		0.902
(1.00) 		0.0467
(1.00) 		0.716
(1.00) 		0.015
(1.00)
18p 59 (16%) 306 0.552
(1.00) 		0.00351
(1.00) 		1
(1.00) 		0.0853
(1.00) 		0.222
(1.00) 		0.184
(1.00) 		0.0607
(1.00) 		0.72
(1.00) 		0.765
(1.00) 		0.0192
(1.00) 		0.551
(1.00) 		0.612
(1.00)
18q 51 (14%) 314 0.0942
(1.00) 		0.0286
(1.00) 		0.32
(1.00) 		0.0474
(1.00) 		0.217
(1.00) 		0.299
(1.00) 		0.00549
(1.00) 		0.347
(1.00) 		0.755
(1.00) 		0.018
(1.00) 		0.78
(1.00) 		0.876
(1.00)
21q 46 (13%) 319 1
(1.00) 		0.0138
(1.00) 		0.262
(1.00) 		0.0568
(1.00) 		0.0912
(1.00) 		0.37
(1.00) 		0.0265
(1.00) 		0.0252
(1.00) 		0.0576
(1.00) 		0.0965
(1.00) 		0.142
(1.00) 		0.271
(1.00)
xq 79 (22%) 286 0.745
(1.00) 		0.0422
(1.00) 		0.533
(1.00) 		0.163
(1.00) 		0.0123
(1.00) 		0.0155
(1.00) 		0.145
(1.00) 		0.018
(1.00) 		0.207
(1.00) 		0.369
(1.00) 		0.0312
(1.00) 		0.0376
(1.00)
'1p' versus 'MRNA_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.25

Table S1.  Gene #1: '1p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 6 10 4
1P MUTATED 7 2 1 1
1P WILD-TYPE 0 4 9 3

Figure S1.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p' versus 'CN_CNMF'

P value = 2.66e-47 (Fisher's exact test), Q value = 1.2e-44

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
1P MUTATED 8 17 117
1P WILD-TYPE 130 70 23

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

'1p' versus 'METHLYATION_CNMF'

P value = 1.49e-64 (Fisher's exact test), Q value = 7e-62

Table S3.  Gene #1: '1p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
1P MUTATED 9 9 107 14
1P WILD-TYPE 152 46 1 22

Figure S3.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p' versus 'MRNASEQ_CNMF'

P value = 2.91e-33 (Chi-square test), Q value = 1.3e-30

Table S4.  Gene #1: '1p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
1P MUTATED 3 13 64 50 3 9
1P WILD-TYPE 91 57 1 59 4 9

Figure S4.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.57e-37 (Fisher's exact test), Q value = 1.2e-34

Table S5.  Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
1P MUTATED 60 21 61
1P WILD-TYPE 1 153 67

Figure S5.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p' versus 'MIRSEQ_CNMF'

P value = 7.46e-08 (Chi-square test), Q value = 3.3e-05

Table S6.  Gene #1: '1p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 61 100 16 49
1P MUTATED 21 10 50 14 18
1P WILD-TYPE 56 51 50 2 31

Figure S6.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.26e-05 (Fisher's exact test), Q value = 0.037

Table S7.  Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 169 132
1P MUTATED 2 47 64
1P WILD-TYPE 0 122 68

Figure S7.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.35e-09 (Chi-square test), Q value = 3.7e-06

Table S8.  Gene #1: '1p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
1P MUTATED 2 13 17 39 22 11 1 8
1P WILD-TYPE 47 34 27 42 6 23 3 8

Figure S8.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.42e-07 (Fisher's exact test), Q value = 0.00015

Table S9.  Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
1P MUTATED 1 44 68
1P WILD-TYPE 9 125 56

Figure S9.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000154 (Fisher's exact test), Q value = 0.062

Table S10.  Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 169 132
2P MUTATED 2 15 3
2P WILD-TYPE 0 154 129

Figure S10.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Chi-square test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
2Q MUTATED 6 6 2 3 3 0
2Q WILD-TYPE 88 64 63 106 4 18

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

'3p' versus 'MRNASEQ_CNMF'

P value = 8.38e-09 (Chi-square test), Q value = 3.7e-06

Table S12.  Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
3P MUTATED 4 8 4 5 5 1
3P WILD-TYPE 90 62 61 104 2 17

Figure S12.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q' versus 'MRNASEQ_CNMF'

P value = 6.32e-08 (Chi-square test), Q value = 2.8e-05

Table S13.  Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
3Q MUTATED 6 8 3 6 5 1
3Q WILD-TYPE 88 62 62 103 2 17

Figure S13.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 9.89e-07 (Fisher's exact test), Q value = 0.00042

Table S14.  Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
4P MUTATED 22 3 36 1
4P WILD-TYPE 139 52 72 35

Figure S14.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p' versus 'MRNASEQ_CNMF'

P value = 7.15e-07 (Chi-square test), Q value = 0.00031

Table S15.  Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
4P MUTATED 11 4 24 17 4 1
4P WILD-TYPE 83 66 41 92 3 17

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

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0055

Table S16.  Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
4P MUTATED 23 17 21
4P WILD-TYPE 38 157 107

Figure S16.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'METHLYATION_CNMF'

P value = 3.84e-06 (Fisher's exact test), Q value = 0.0016

Table S17.  Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
4Q MUTATED 28 3 39 3
4Q WILD-TYPE 133 52 69 33

Figure S17.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q' versus 'MRNASEQ_CNMF'

P value = 2.56e-06 (Chi-square test), Q value = 0.0011

Table S18.  Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
4Q MUTATED 14 4 26 22 4 2
4Q WILD-TYPE 80 66 39 87 3 16

Figure S18.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.08e-06 (Fisher's exact test), Q value = 0.0017

Table S19.  Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
4Q MUTATED 25 19 28
4Q WILD-TYPE 36 155 100

Figure S19.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000436 (Chi-square test), Q value = 0.17

Table S20.  Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
4Q MUTATED 2 4 15 17 11 8 1 1
4Q WILD-TYPE 47 43 29 64 17 26 3 15

Figure S20.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p' versus 'CN_CNMF'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.00086

Table S21.  Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
5P MUTATED 22 11 1
5P WILD-TYPE 116 76 139

Figure S21.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

'5p' versus 'METHLYATION_CNMF'

P value = 5.21e-05 (Fisher's exact test), Q value = 0.021

Table S22.  Gene #9: '5p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
5P MUTATED 26 6 1 1
5P WILD-TYPE 135 49 107 35

Figure S22.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p' versus 'MRNASEQ_CNMF'

P value = 4.64e-05 (Chi-square test), Q value = 0.019

Table S23.  Gene #9: '5p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
5P MUTATED 9 9 1 7 4 3
5P WILD-TYPE 85 61 64 102 3 15

Figure S23.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q' versus 'CN_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.049

Table S24.  Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
5Q MUTATED 19 10 2
5Q WILD-TYPE 119 77 138

Figure S24.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 0.000257 (Fisher's exact test), Q value = 0.1

Table S25.  Gene #10: '5q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
5Q MUTATED 23 6 1 1
5Q WILD-TYPE 138 49 107 35

Figure S25.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q' versus 'MRNASEQ_CNMF'

P value = 2.7e-10 (Chi-square test), Q value = 1.2e-07

Table S26.  Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
5Q MUTATED 8 11 1 2 5 3
5Q WILD-TYPE 86 59 64 107 2 15

Figure S26.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000326 (Fisher's exact test), Q value = 0.13

Table S27.  Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
5Q MUTATED 0 24 6
5Q WILD-TYPE 61 150 122

Figure S27.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q' versus 'CN_CNMF'

P value = 0.000247 (Fisher's exact test), Q value = 0.097

Table S28.  Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
6Q MUTATED 22 21 8
6Q WILD-TYPE 116 66 132

Figure S28.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 4.4e-28 (Fisher's exact test), Q value = 2e-25

Table S29.  Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
7P MUTATED 21 62 8
7P WILD-TYPE 117 25 132

Figure S29.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 2.31e-15 (Fisher's exact test), Q value = 1e-12

Table S30.  Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
7P MUTATED 30 40 13 6
7P WILD-TYPE 131 15 95 30

Figure S30.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p' versus 'RPPA_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S31.  Gene #13: '7p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
7P MUTATED 13 28 12 11
7P WILD-TYPE 39 34 56 63

Figure S31.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 2.8e-12 (Chi-square test), Q value = 1.3e-09

Table S32.  Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
7P MUTATED 17 41 7 19 4 1
7P WILD-TYPE 77 29 58 90 3 17

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

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.45e-06 (Fisher's exact test), Q value = 0.0031

Table S33.  Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
7P MUTATED 6 62 21
7P WILD-TYPE 55 112 107

Figure S33.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.29e-05 (Chi-square test), Q value = 0.0054

Table S34.  Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
7P MUTATED 9 25 13 11 4 13 1 1
7P WILD-TYPE 40 22 31 70 24 21 3 15

Figure S34.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.9e-07 (Fisher's exact test), Q value = 3e-04

Table S35.  Gene #13: '7p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
7P MUTATED 8 53 16
7P WILD-TYPE 2 116 108

Figure S35.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 2.04e-28 (Fisher's exact test), Q value = 9.4e-26

Table S36.  Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
7Q MUTATED 31 70 15
7Q WILD-TYPE 107 17 125

Figure S36.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 5.95e-14 (Fisher's exact test), Q value = 2.7e-11

Table S37.  Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
7Q MUTATED 45 43 19 7
7Q WILD-TYPE 116 12 89 29

Figure S37.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 2.31e-08 (Chi-square test), Q value = 1e-05

Table S38.  Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
7Q MUTATED 28 43 10 26 4 3
7Q WILD-TYPE 66 27 55 83 3 15

Figure S38.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.08e-06 (Fisher's exact test), Q value = 0.0017

Table S39.  Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
7Q MUTATED 9 76 29
7Q WILD-TYPE 52 98 99

Figure S39.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000523 (Chi-square test), Q value = 0.2

Table S40.  Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
7Q MUTATED 12 26 17 16 8 16 1 2
7Q WILD-TYPE 37 21 27 65 20 18 3 14

Figure S40.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.017

Table S41.  Gene #14: '7q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
7Q MUTATED 8 64 26
7Q WILD-TYPE 2 105 98

Figure S41.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p' versus 'CN_CNMF'

P value = 5.53e-05 (Fisher's exact test), Q value = 0.022

Table S42.  Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
8P MUTATED 23 15 4
8P WILD-TYPE 115 72 136

Figure S42.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'CN_CNMF'

P value = 1.51e-05 (Fisher's exact test), Q value = 0.0063

Table S43.  Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
8Q MUTATED 25 16 4
8Q WILD-TYPE 113 71 136

Figure S43.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000286 (Fisher's exact test), Q value = 0.11

Table S44.  Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
8Q MUTATED 1 33 11
8Q WILD-TYPE 60 141 117

Figure S44.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S45.  Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
8Q MUTATED 2 33 6
8Q WILD-TYPE 8 136 118

Figure S45.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p' versus 'MRNASEQ_CNMF'

P value = 0.000494 (Chi-square test), Q value = 0.19

Table S46.  Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
9P MUTATED 24 20 12 28 7 4
9P WILD-TYPE 70 50 53 81 0 14

Figure S46.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q' versus 'MRNASEQ_CNMF'

P value = 0.000401 (Chi-square test), Q value = 0.15

Table S47.  Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
9Q MUTATED 9 12 11 12 5 2
9Q WILD-TYPE 85 58 54 97 2 16

Figure S47.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'CN_CNMF'

P value = 2.33e-18 (Fisher's exact test), Q value = 1.1e-15

Table S48.  Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
10P MUTATED 36 50 7
10P WILD-TYPE 102 37 133

Figure S48.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 2.69e-26 (Fisher's exact test), Q value = 1.2e-23

Table S49.  Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
10P MUTATED 35 47 6 4
10P WILD-TYPE 126 8 102 32

Figure S49.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p' versus 'RPPA_CNMF'

P value = 2.03e-05 (Fisher's exact test), Q value = 0.0084

Table S50.  Gene #19: '10p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
10P MUTATED 15 29 11 9
10P WILD-TYPE 37 33 57 65

Figure S50.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 2.51e-16 (Chi-square test), Q value = 1.1e-13

Table S51.  Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
10P MUTATED 19 45 2 19 4 3
10P WILD-TYPE 75 25 63 90 3 15

Figure S51.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.14e-11 (Fisher's exact test), Q value = 3.6e-08

Table S52.  Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
10P MUTATED 2 70 20
10P WILD-TYPE 59 104 108

Figure S52.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CNMF'

P value = 0.000657 (Chi-square test), Q value = 0.25

Table S53.  Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 61 100 16 49
10P MUTATED 30 23 16 1 11
10P WILD-TYPE 47 38 84 15 38

Figure S53.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.31e-07 (Chi-square test), Q value = 5.7e-05

Table S54.  Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
10P MUTATED 12 30 8 14 2 9 2 4
10P WILD-TYPE 37 17 36 67 26 25 2 12

Figure S54.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.56e-07 (Fisher's exact test), Q value = 0.00011

Table S55.  Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
10P MUTATED 7 59 15
10P WILD-TYPE 3 110 109

Figure S55.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 6.69e-24 (Fisher's exact test), Q value = 3.1e-21

Table S56.  Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
10Q MUTATED 15 53 6
10Q WILD-TYPE 123 34 134

Figure S56.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 3.17e-30 (Fisher's exact test), Q value = 1.5e-27

Table S57.  Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
10Q MUTATED 17 47 6 3
10Q WILD-TYPE 144 8 102 33

Figure S57.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q' versus 'RPPA_CNMF'

P value = 2e-06 (Fisher's exact test), Q value = 0.00085

Table S58.  Gene #20: '10q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
10Q MUTATED 7 28 9 7
10Q WILD-TYPE 45 34 59 67

Figure S58.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000399 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #20: '10q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 129 119
10Q MUTATED 1 38 12
10Q WILD-TYPE 7 91 107

Figure S59.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q' versus 'MRNASEQ_CNMF'

P value = 4.77e-23 (Chi-square test), Q value = 2.2e-20

Table S60.  Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
10Q MUTATED 6 45 2 16 3 1
10Q WILD-TYPE 88 25 63 93 4 17

Figure S60.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-07 (Fisher's exact test), Q value = 4.9e-05

Table S61.  Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
10Q MUTATED 2 55 16
10Q WILD-TYPE 59 119 112

Figure S61.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.36e-11 (Chi-square test), Q value = 1.1e-08

Table S62.  Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
10Q MUTATED 3 29 4 12 2 11 1 3
10Q WILD-TYPE 46 18 40 69 26 23 3 13

Figure S62.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.0069

Table S63.  Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
10Q MUTATED 7 44 14
10Q WILD-TYPE 3 125 110

Figure S63.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 8.12e-06 (Fisher's exact test), Q value = 0.0034

Table S64.  Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
12Q MUTATED 32 8 6
12Q WILD-TYPE 106 79 134

Figure S64.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

'13q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000618 (Fisher's exact test), Q value = 0.23

Table S65.  Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 6 10 4
13Q MUTATED 0 0 5 4
13Q WILD-TYPE 7 6 5 0

Figure S65.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.092

Table S66.  Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
14Q MUTATED 15 27 17
14Q WILD-TYPE 123 60 123

Figure S66.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 0.000195 (Chi-square test), Q value = 0.078

Table S67.  Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
14Q MUTATED 8 24 7 15 2 2
14Q WILD-TYPE 86 46 58 94 5 16

Figure S67.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000426 (Chi-square test), Q value = 0.16

Table S68.  Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
14Q MUTATED 5 20 6 10 3 4 1 3
14Q WILD-TYPE 44 27 38 71 25 30 3 13

Figure S68.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q' versus 'MRNASEQ_CNMF'

P value = 0.000272 (Chi-square test), Q value = 0.11

Table S69.  Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
15Q MUTATED 7 9 15 5 3 1
15Q WILD-TYPE 87 61 50 104 4 17

Figure S69.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 1.61e-06 (Chi-square test), Q value = 0.00069

Table S70.  Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
16P MUTATED 2 5 4 6 4 1
16P WILD-TYPE 92 65 61 103 3 17

Figure S70.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000297 (Fisher's exact test), Q value = 0.12

Table S71.  Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 169 132
16P MUTATED 2 6 13
16P WILD-TYPE 0 163 119

Figure S71.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MRNASEQ_CNMF'

P value = 7.48e-08 (Chi-square test), Q value = 3.3e-05

Table S72.  Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
17P MUTATED 3 10 4 2 4 1
17P WILD-TYPE 91 60 61 107 3 17

Figure S72.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000222 (Fisher's exact test), Q value = 0.088

Table S73.  Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 169 132
17P MUTATED 2 17 4
17P WILD-TYPE 0 152 128

Figure S73.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q' versus 'MRNASEQ_CNMF'

P value = 0.000163 (Chi-square test), Q value = 0.065

Table S74.  Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
17Q MUTATED 3 7 5 2 3 1
17Q WILD-TYPE 91 63 60 107 4 17

Figure S74.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p' versus 'CN_CNMF'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.011

Table S75.  Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
19P MUTATED 14 27 41
19P WILD-TYPE 124 60 99

Figure S75.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 3.12e-08 (Fisher's exact test), Q value = 1.4e-05

Table S76.  Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
19P MUTATED 16 22 38 4
19P WILD-TYPE 145 33 70 32

Figure S76.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p' versus 'MRNASEQ_CNMF'

P value = 0.00051 (Chi-square test), Q value = 0.19

Table S77.  Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
19P MUTATED 8 22 24 23 2 3
19P WILD-TYPE 86 48 41 86 5 15

Figure S77.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q' versus 'CN_CNMF'

P value = 6.79e-42 (Fisher's exact test), Q value = 3.2e-39

Table S78.  Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
19Q MUTATED 17 26 123
19Q WILD-TYPE 121 61 17

Figure S78.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'19q' versus 'METHLYATION_CNMF'

P value = 1.16e-50 (Fisher's exact test), Q value = 5.4e-48

Table S79.  Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
19Q MUTATED 22 18 107 15
19Q WILD-TYPE 139 37 1 21

Figure S79.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q' versus 'MRNASEQ_CNMF'

P value = 1.42e-25 (Chi-square test), Q value = 6.5e-23

Table S80.  Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
19Q MUTATED 12 20 64 56 2 11
19Q WILD-TYPE 82 50 1 53 5 7

Figure S80.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.25e-29 (Fisher's exact test), Q value = 1.5e-26

Table S81.  Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
19Q MUTATED 60 37 68
19Q WILD-TYPE 1 137 60

Figure S81.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_CNMF'

P value = 0.000207 (Chi-square test), Q value = 0.082

Table S82.  Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 61 100 16 49
19Q MUTATED 23 22 55 13 20
19Q WILD-TYPE 54 39 45 3 29

Figure S82.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000572 (Fisher's exact test), Q value = 0.22

Table S83.  Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 169 132
19Q MUTATED 0 60 73
19Q WILD-TYPE 2 109 59

Figure S83.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.58e-07 (Chi-square test), Q value = 0.00011

Table S84.  Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
19Q MUTATED 4 18 22 42 22 14 2 9
19Q WILD-TYPE 45 29 22 39 6 20 2 7

Figure S84.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.22e-05 (Fisher's exact test), Q value = 0.017

Table S85.  Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
19Q MUTATED 3 57 73
19Q WILD-TYPE 7 112 51

Figure S85.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 1.5e-08 (Fisher's exact test), Q value = 6.6e-06

Table S86.  Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
20P MUTATED 10 24 3
20P WILD-TYPE 128 63 137

Figure S86.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 6.54e-09 (Fisher's exact test), Q value = 2.9e-06

Table S87.  Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
20P MUTATED 11 21 4 1
20P WILD-TYPE 150 34 104 35

Figure S87.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 2.13e-06 (Chi-square test), Q value = 9e-04

Table S88.  Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
20P MUTATED 5 18 3 8 3 0
20P WILD-TYPE 89 52 62 101 4 18

Figure S88.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'CN_CNMF'

P value = 7.58e-08 (Fisher's exact test), Q value = 3.3e-05

Table S89.  Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 87 140
20Q MUTATED 8 23 4
20Q WILD-TYPE 130 64 136

Figure S89.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 1.03e-10 (Fisher's exact test), Q value = 4.6e-08

Table S90.  Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 55 108 36
20Q MUTATED 9 22 4 0
20Q WILD-TYPE 152 33 104 36

Figure S90.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q' versus 'MRNASEQ_CNMF'

P value = 7.85e-09 (Chi-square test), Q value = 3.5e-06

Table S91.  Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
20Q MUTATED 4 21 3 5 2 0
20Q WILD-TYPE 90 49 62 104 5 18

Figure S91.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.17e-05 (Fisher's exact test), Q value = 0.021

Table S92.  Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 174 128
20Q MUTATED 1 29 5
20Q WILD-TYPE 60 145 123

Figure S92.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.62e-05 (Chi-square test), Q value = 0.019

Table S93.  Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 49 47 44 81 28 34 4 16
20Q MUTATED 1 12 4 1 2 8 1 1
20Q WILD-TYPE 48 35 40 80 26 26 3 15

Figure S93.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000242 (Fisher's exact test), Q value = 0.095

Table S94.  Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 169 124
20Q MUTATED 4 22 4
20Q WILD-TYPE 6 147 120

Figure S94.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q' versus 'RPPA_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.078

Table S95.  Gene #39: '22q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
22Q MUTATED 3 20 7 6
22Q WILD-TYPE 49 42 61 68

Figure S95.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 0.000215 (Chi-square test), Q value = 0.085

Table S96.  Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 94 70 65 109 7 18
22Q MUTATED 7 20 9 10 3 1
22Q WILD-TYPE 87 50 56 99 4 17

Figure S96.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 365

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

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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