Correlation between copy number variation genes (focal events) and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1V123NP
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 52 focal events and 12 molecular subtypes across 513 patients, 197 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q22 cnv correlated to 'CN_CNMF'.

  • amp_1q32.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.33 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_4q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_7p11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q31.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q32.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_12p13.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_12q14.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_15q26.3 cnv correlated to 'CN_CNMF'.

  • amp_19p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xp11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_xp11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_1p36.32 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p32.3 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'.

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

  • del_3p21.31 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • del_3q13.31 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_3q29 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_4q34.3 cnv correlated to 'METHLYATION_CNMF'.

  • del_5p15.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_5q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_6p25.3 cnv correlated to 'CN_CNMF'.

  • del_6q22.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • del_10q26.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11p15.5 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_11p15.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_12q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_13q14.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_13q34 cnv correlated to 'CN_CNMF'.

  • del_14q24.3 cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_19q13.41 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19q13.42 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_22q13.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 52 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, 197 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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 1p36 32 206 (40%) 307 0.00045
(0.188)
0.00015
(0.0652)
1e-05
(0.00604)
1e-05
(0.00604)
0.00067
(0.273)
0.846
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
del 1p32 3 196 (38%) 317 0.0288
(1.00)
0.00017
(0.0734)
1e-05
(0.00604)
1e-05
(0.00604)
0.00057
(0.234)
0.614
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
del 10q26 3 151 (29%) 362 0.0838
(1.00)
0.705
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
0.00026
(0.11)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
amp 7p11 2 128 (25%) 385 0.763
(1.00)
0.404
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
5e-05
(0.0226)
0.0125
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00042
(0.176)
1e-05
(0.00604)
4e-05
(0.0183)
1e-05
(0.00604)
del 9p21 3 176 (34%) 337 0.335
(1.00)
0.0625
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
2e-05
(0.00944)
1e-05
(0.00604)
1e-05
(0.00604)
0.251
(1.00)
1e-05
(0.00604)
0.00084
(0.336)
1e-05
(0.00604)
del 19q13 41 267 (52%) 246 0.0338
(1.00)
0.01
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00092
(0.367)
0.185
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
del 19q13 42 278 (54%) 235 0.0362
(1.00)
0.0213
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00229
(0.859)
0.575
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
1e-05
(0.00604)
del 22q13 31 77 (15%) 436 0.252
(1.00)
0.0422
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00029
(0.123)
0.0119
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0353
(1.00)
3e-05
(0.0139)
0.00165
(0.63)
4e-05
(0.0183)
amp 1q32 1 43 (8%) 470 1e-05
(0.00604)
1e-05
(0.00604)
0.164
(1.00)
0.354
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.252
(1.00)
2e-05
(0.00944)
0.00137
(0.534)
1e-05
(0.00604)
amp 7q31 2 174 (34%) 339 1
(1.00)
0.812
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0041
(1.00)
0.188
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0112
(1.00)
1e-05
(0.00604)
0.00879
(1.00)
1e-05
(0.00604)
amp 7q32 3 182 (35%) 331 0.697
(1.00)
1
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00675
(1.00)
0.166
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0546
(1.00)
1e-05
(0.00604)
0.0222
(1.00)
1e-05
(0.00604)
amp 12q14 1 37 (7%) 476 1e-05
(0.00604)
2e-05
(0.00944)
0.0157
(1.00)
0.729
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0028
(1.00)
1e-05
(0.00604)
0.0427
(1.00)
1e-05
(0.00604)
amp 19p13 2 122 (24%) 391 0.0749
(1.00)
0.15
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.276
(1.00)
0.201
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00023
(0.0982)
0.142
(1.00)
0.0419
(1.00)
0.00052
(0.216)
del 11p15 5 104 (20%) 409 0.644
(1.00)
0.00051
(0.212)
1e-05
(0.00604)
1e-05
(0.00604)
0.146
(1.00)
0.632
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
2e-05
(0.00944)
0.00474
(1.00)
0.99
(1.00)
0.888
(1.00)
del 11p15 1 72 (14%) 441 1
(1.00)
0.0309
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0126
(1.00)
0.792
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
5e-05
(0.0226)
3e-05
(0.0139)
0.874
(1.00)
0.0336
(1.00)
amp 4q12 30 (6%) 483 1
(1.00)
0.0422
(1.00)
0.0002
(0.0858)
0.00018
(0.0776)
0.00872
(1.00)
0.278
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00339
(1.00)
0.00013
(0.0569)
0.944
(1.00)
0.00379
(1.00)
amp 8q24 13 100 (19%) 413 0.369
(1.00)
0.239
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0415
(1.00)
0.485
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0289
(1.00)
0.00096
(0.382)
0.112
(1.00)
2e-05
(0.00944)
amp 10p15 3 71 (14%) 442 0.526
(1.00)
0.0833
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0293
(1.00)
0.135
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00105
(0.416)
0.0773
(1.00)
0.333
(1.00)
0.00011
(0.0485)
amp 19p13 3 129 (25%) 384 0.075
(1.00)
0.149
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.884
(1.00)
0.579
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00012
(0.0528)
0.157
(1.00)
0.0457
(1.00)
0.00083
(0.333)
amp xp11 22 63 (12%) 450 0.649
(1.00)
1
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0265
(1.00)
0.39
(1.00)
2e-05
(0.00944)
1e-05
(0.00604)
0.00033
(0.139)
0.352
(1.00)
0.0741
(1.00)
0.00946
(1.00)
del 5q34 64 (12%) 449 0.444
(1.00)
0.235
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.163
(1.00)
1
(1.00)
8e-05
(0.0357)
1e-05
(0.00604)
2e-05
(0.00944)
0.146
(1.00)
0.613
(1.00)
0.666
(1.00)
del 6q24 3 82 (16%) 431 0.171
(1.00)
0.28
(1.00)
0.0003
(0.127)
1e-05
(0.00604)
0.0989
(1.00)
0.62
(1.00)
0.00145
(0.563)
9e-05
(0.04)
0.00013
(0.0569)
0.164
(1.00)
0.0213
(1.00)
4e-05
(0.0183)
del 13q14 2 142 (28%) 371 0.179
(1.00)
7e-05
(0.0314)
1e-05
(0.00604)
6e-05
(0.0271)
0.0343
(1.00)
0.605
(1.00)
0.0002
(0.0858)
2e-05
(0.00944)
0.0183
(1.00)
0.00572
(1.00)
0.475
(1.00)
0.413
(1.00)
del 13q14 2 144 (28%) 369 0.181
(1.00)
6e-05
(0.0271)
1e-05
(0.00604)
3e-05
(0.0139)
0.0327
(1.00)
0.709
(1.00)
0.00014
(0.061)
3e-05
(0.0139)
0.0162
(1.00)
0.00337
(1.00)
0.433
(1.00)
0.361
(1.00)
amp 12p13 32 72 (14%) 441 0.865
(1.00)
0.097
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.114
(1.00)
0.191
(1.00)
0.00018
(0.0776)
4e-05
(0.0183)
0.0101
(1.00)
0.00647
(1.00)
0.0243
(1.00)
0.0853
(1.00)
del 2q37 3 77 (15%) 436 0.367
(1.00)
0.0128
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.00472
(1.00)
0.0201
(1.00)
0.00024
(0.102)
7e-05
(0.0314)
0.0148
(1.00)
0.141
(1.00)
0.103
(1.00)
0.0825
(1.00)
del 6q22 31 78 (15%) 435 0.617
(1.00)
0.579
(1.00)
6e-05
(0.0271)
2e-05
(0.00944)
0.115
(1.00)
0.509
(1.00)
0.00514
(1.00)
0.00053
(0.219)
0.00075
(0.301)
0.121
(1.00)
0.0064
(1.00)
2e-05
(0.00944)
amp xp11 22 48 (9%) 465 0.649
(1.00)
1
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.319
(1.00)
0.73
(1.00)
0.00152
(0.585)
8e-05
(0.0357)
0.0561
(1.00)
0.598
(1.00)
0.329
(1.00)
0.108
(1.00)
del 8q24 3 29 (6%) 484 1e-05
(0.00604)
1e-05
(0.00604)
0.927
(1.00)
0.464
(1.00)
0.00165
(0.63)
0.00059
(0.241)
0.00411
(1.00)
0.00329
(1.00)
0.166
(1.00)
0.0314
(1.00)
del 14q24 3 121 (24%) 392 0.304
(1.00)
0.0977
(1.00)
0.00482
(1.00)
0.0122
(1.00)
0.00159
(0.609)
0.0359
(1.00)
0.00054
(0.223)
9e-05
(0.04)
0.00031
(0.131)
0.0046
(1.00)
0.00169
(0.642)
0.00112
(0.442)
amp 3q26 33 21 (4%) 492 1
(1.00)
0.582
(1.00)
1e-05
(0.00604)
0.00122
(0.477)
0.147
(1.00)
0.849
(1.00)
0.00072
(0.29)
0.00028
(0.119)
0.00146
(0.565)
0.0183
(1.00)
0.0529
(1.00)
0.00359
(1.00)
del 3p21 31 49 (10%) 464 1
(1.00)
0.00684
(1.00)
0.00015
(0.0652)
0.00199
(0.748)
0.00235
(0.877)
0.263
(1.00)
0.0231
(1.00)
0.00605
(1.00)
0.00054
(0.223)
0.00232
(0.868)
0.729
(1.00)
0.0501
(1.00)
del 3q13 31 39 (8%) 474 0.175
(1.00)
0.881
(1.00)
0.00012
(0.0528)
0.00381
(1.00)
0.341
(1.00)
0.174
(1.00)
0.162
(1.00)
0.0317
(1.00)
0.156
(1.00)
0.00057
(0.234)
0.574
(1.00)
0.113
(1.00)
del 3q29 47 (9%) 466 0.175
(1.00)
0.882
(1.00)
1e-05
(0.00604)
0.00042
(0.176)
0.405
(1.00)
0.921
(1.00)
0.00452
(1.00)
0.00112
(0.442)
0.128
(1.00)
0.0047
(1.00)
0.692
(1.00)
0.171
(1.00)
del 5p15 33 50 (10%) 463 1
(1.00)
0.0679
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.865
(1.00)
0.581
(1.00)
0.00472
(1.00)
0.00068
(0.276)
0.00192
(0.724)
0.205
(1.00)
0.947
(1.00)
0.441
(1.00)
del 9p23 150 (29%) 363 0.446
(1.00)
0.657
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.0395
(1.00)
0.0025
(0.927)
0.0132
(1.00)
0.021
(1.00)
0.917
(1.00)
0.114
(1.00)
0.41
(1.00)
0.00278
(1.00)
del 12q12 72 (14%) 441 1
(1.00)
0.151
(1.00)
1e-05
(0.00604)
1e-05
(0.00604)
0.912
(1.00)
0.284
(1.00)
0.00645
(1.00)
0.00338
(1.00)
0.0133
(1.00)
0.497
(1.00)
0.909
(1.00)
0.963
(1.00)
amp 1q22 42 (8%) 471 0.00057
(0.234)
0.00744
(1.00)
0.249
(1.00)
0.883
(1.00)
0.00154
(0.591)
0.0143
(1.00)
0.574
(1.00)
0.0891
(1.00)
0.154
(1.00)
0.313
(1.00)
amp 15q26 3 19 (4%) 494 1
(1.00)
0.0432
(1.00)
4e-05
(0.0183)
0.00096
(0.382)
0.22
(1.00)
0.606
(1.00)
0.044
(1.00)
0.00858
(1.00)
0.497
(1.00)
0.284
(1.00)
0.592
(1.00)
0.19
(1.00)
del 4q34 3 138 (27%) 375 1
(1.00)
0.357
(1.00)
0.0128
(1.00)
1e-05
(0.00604)
0.165
(1.00)
0.225
(1.00)
0.0542
(1.00)
0.0725
(1.00)
0.0305
(1.00)
0.0376
(1.00)
0.00121
(0.474)
0.00587
(1.00)
del 6p25 3 50 (10%) 463 0.00016
(0.0693)
0.0424
(1.00)
0.231
(1.00)
0.926
(1.00)
0.0684
(1.00)
0.113
(1.00)
0.413
(1.00)
0.253
(1.00)
0.144
(1.00)
0.0864
(1.00)
del 13q34 110 (21%) 403 0.506
(1.00)
0.151
(1.00)
0.0001
(0.0442)
0.0119
(1.00)
0.0855
(1.00)
0.76
(1.00)
0.00984
(1.00)
0.00189
(0.714)
0.0258
(1.00)
0.00313
(1.00)
0.311
(1.00)
0.177
(1.00)
amp 2p24 3 24 (5%) 489 0.618
(1.00)
0.583
(1.00)
0.00243
(0.904)
0.0333
(1.00)
0.491
(1.00)
1
(1.00)
0.0245
(1.00)
0.0142
(1.00)
0.72
(1.00)
0.0344
(1.00)
0.44
(1.00)
0.115
(1.00)
amp 9q34 3 46 (9%) 467 0.511
(1.00)
0.884
(1.00)
0.0948
(1.00)
0.0491
(1.00)
0.209
(1.00)
0.761
(1.00)
0.0802
(1.00)
0.0141
(1.00)
0.201
(1.00)
0.0857
(1.00)
0.283
(1.00)
0.285
(1.00)
amp 11q24 1 87 (17%) 426 0.0714
(1.00)
0.12
(1.00)
0.613
(1.00)
0.0112
(1.00)
0.0542
(1.00)
0.0294
(1.00)
0.0703
(1.00)
0.0653
(1.00)
0.76
(1.00)
0.115
(1.00)
0.853
(1.00)
0.044
(1.00)
amp 13q34 22 (4%) 491 0.00151
(0.583)
0.00137
(0.534)
0.187
(1.00)
0.718
(1.00)
0.0434
(1.00)
0.00953
(1.00)
0.296
(1.00)
0.688
(1.00)
0.962
(1.00)
0.0504
(1.00)
amp 17q25 1 44 (9%) 469 0.0543
(1.00)
0.36
(1.00)
0.331
(1.00)
0.44
(1.00)
0.0595
(1.00)
0.0695
(1.00)
0.15
(1.00)
0.564
(1.00)
0.187
(1.00)
0.563
(1.00)
del 1q43 31 (6%) 482 0.315
(1.00)
0.00974
(1.00)
0.101
(1.00)
0.535
(1.00)
0.028
(1.00)
0.0132
(1.00)
0.228
(1.00)
0.759
(1.00)
0.793
(1.00)
0.302
(1.00)
del 7p22 3 23 (4%) 490 0.0254
(1.00)
0.123
(1.00)
0.256
(1.00)
0.355
(1.00)
0.576
(1.00)
0.582
(1.00)
0.503
(1.00)
0.0953
(1.00)
0.733
(1.00)
0.354
(1.00)
del 12p13 1 38 (7%) 475 0.0007
(0.283)
0.00184
(0.697)
0.152
(1.00)
1
(1.00)
0.00762
(1.00)
0.0133
(1.00)
0.0575
(1.00)
0.0432
(1.00)
0.955
(1.00)
0.252
(1.00)
del 18q23 78 (15%) 435 0.322
(1.00)
0.329
(1.00)
0.459
(1.00)
0.00332
(1.00)
0.462
(1.00)
0.0751
(1.00)
0.399
(1.00)
0.0792
(1.00)
0.346
(1.00)
0.618
(1.00)
0.53
(1.00)
0.899
(1.00)
del xq21 1 78 (15%) 435 0.84
(1.00)
0.267
(1.00)
0.193
(1.00)
0.0524
(1.00)
0.0525
(1.00)
0.154
(1.00)
0.00756
(1.00)
0.00068
(0.276)
0.00119
(0.468)
0.356
(1.00)
0.118
(1.00)
0.156
(1.00)
'amp_1q22' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.23

Table S1.  Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 1(1Q22) MUTATED 15 19 8
AMP PEAK 1(1Q22) WILD-TYPE 157 101 213

Figure S1.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S2.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 2(1Q32.1) MUTATED 10 28 5
AMP PEAK 2(1Q32.1) WILD-TYPE 162 92 216

Figure S2.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S3.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 2(1Q32.1) MUTATED 12 24 6 1
AMP PEAK 2(1Q32.1) WILD-TYPE 213 57 161 39

Figure S3.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S4.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 2(1Q32.1) MUTATED 2 26 1 12 2
AMP PEAK 2(1Q32.1) WILD-TYPE 133 86 107 116 26

Figure S4.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S5.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 2(1Q32.1) MUTATED 3 24 5 11
AMP PEAK 2(1Q32.1) WILD-TYPE 132 89 120 127

Figure S5.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S6.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 2(1Q32.1) MUTATED 8 13 22
AMP PEAK 2(1Q32.1) WILD-TYPE 214 171 81

Figure S6.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S7.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 2(1Q32.1) MUTATED 5 3 14 21
AMP PEAK 2(1Q32.1) WILD-TYPE 86 134 174 68

Figure S7.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S8.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 4(3Q26.33) MUTATED 1 17 3
AMP PEAK 4(3Q26.33) WILD-TYPE 171 103 218

Figure S8.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.12

Table S9.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 4(3Q26.33) MUTATED 4 13 1 3
AMP PEAK 4(3Q26.33) WILD-TYPE 131 100 124 135

Figure S9.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.086

Table S10.  Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 5(4Q12) MUTATED 17 10 3
AMP PEAK 5(4Q12) WILD-TYPE 155 110 218

Figure S10.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.078

Table S11.  Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 5(4Q12) MUTATED 19 9 1 1
AMP PEAK 5(4Q12) WILD-TYPE 206 72 166 39

Figure S11.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S12.  Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 5(4Q12) MUTATED 5 18 0 6 1
AMP PEAK 5(4Q12) WILD-TYPE 130 94 108 122 27

Figure S12.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S13.  Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 5(4Q12) MUTATED 5 19 0 6
AMP PEAK 5(4Q12) WILD-TYPE 130 94 125 132

Figure S13.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.057

Table S14.  Gene #5: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 5(4Q12) MUTATED 7 7 16
AMP PEAK 5(4Q12) WILD-TYPE 215 177 87

Figure S14.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S15.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 6(7P11.2) MUTATED 21 98 9
AMP PEAK 6(7P11.2) WILD-TYPE 151 22 212

Figure S15.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S16.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 6(7P11.2) MUTATED 40 64 15 9
AMP PEAK 6(7P11.2) WILD-TYPE 185 17 152 31

Figure S16.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S17.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
AMP PEAK 6(7P11.2) MUTATED 13 31 12 12
AMP PEAK 6(7P11.2) WILD-TYPE 39 31 56 62

Figure S17.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S18.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 6(7P11.2) MUTATED 22 66 9 24 5
AMP PEAK 6(7P11.2) WILD-TYPE 113 46 99 104 23

Figure S18.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S19.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 6(7P11.2) MUTATED 19 65 10 32
AMP PEAK 6(7P11.2) WILD-TYPE 116 48 115 106

Figure S19.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.18

Table S20.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 6(7P11.2) MUTATED 44 37 32 13
AMP PEAK 6(7P11.2) WILD-TYPE 93 70 151 69

Figure S20.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S21.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 6(7P11.2) MUTATED 37 28 61
AMP PEAK 6(7P11.2) WILD-TYPE 185 156 42

Figure S21.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S22.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
AMP PEAK 6(7P11.2) MUTATED 66 26 33
AMP PEAK 6(7P11.2) WILD-TYPE 119 135 126

Figure S22.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S23.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 6(7P11.2) MUTATED 13 22 32 58
AMP PEAK 6(7P11.2) WILD-TYPE 78 115 156 31

Figure S23.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S24.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 7(7Q31.2) MUTATED 46 105 23
AMP PEAK 7(7Q31.2) WILD-TYPE 126 15 198

Figure S24.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S25.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 7(7Q31.2) MUTATED 77 59 29 9
AMP PEAK 7(7Q31.2) WILD-TYPE 148 22 138 31

Figure S25.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S26.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 7(7Q31.2) MUTATED 48 63 15 38 8
AMP PEAK 7(7Q31.2) WILD-TYPE 87 49 93 90 20

Figure S26.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S27.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 7(7Q31.2) MUTATED 44 61 20 47
AMP PEAK 7(7Q31.2) WILD-TYPE 91 52 105 91

Figure S27.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S28.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 7(7Q31.2) MUTATED 65 48 59
AMP PEAK 7(7Q31.2) WILD-TYPE 157 136 44

Figure S28.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S29.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 7(7Q31.2) MUTATED 24 35 57 55
AMP PEAK 7(7Q31.2) WILD-TYPE 67 102 131 34

Figure S29.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S30.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 8(7Q32.3) MUTATED 49 108 25
AMP PEAK 8(7Q32.3) WILD-TYPE 123 12 196

Figure S30.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S31.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 8(7Q32.3) MUTATED 82 60 30 10
AMP PEAK 8(7Q32.3) WILD-TYPE 143 21 137 30

Figure S31.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S32.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 8(7Q32.3) MUTATED 52 63 16 41 8
AMP PEAK 8(7Q32.3) WILD-TYPE 83 49 92 87 20

Figure S32.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S33.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 8(7Q32.3) MUTATED 47 61 21 51
AMP PEAK 8(7Q32.3) WILD-TYPE 88 52 104 87

Figure S33.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S34.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 8(7Q32.3) MUTATED 68 52 60
AMP PEAK 8(7Q32.3) WILD-TYPE 154 132 43

Figure S34.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S35.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 8(7Q32.3) MUTATED 28 37 59 55
AMP PEAK 8(7Q32.3) WILD-TYPE 63 100 129 34

Figure S35.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S36.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 9(8Q24.13) MUTATED 66 19 15
AMP PEAK 9(8Q24.13) WILD-TYPE 106 101 206

Figure S36.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S37.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 9(8Q24.13) MUTATED 82 4 10 4
AMP PEAK 9(8Q24.13) WILD-TYPE 143 77 157 36

Figure S37.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S38.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 9(8Q24.13) MUTATED 51 12 5 25 6
AMP PEAK 9(8Q24.13) WILD-TYPE 84 100 103 103 22

Figure S38.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S39.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 9(8Q24.13) MUTATED 52 12 7 28
AMP PEAK 9(8Q24.13) WILD-TYPE 83 101 118 110

Figure S39.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S40.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 9(8Q24.13) MUTATED 34 21 35 8
AMP PEAK 9(8Q24.13) WILD-TYPE 57 116 153 81

Figure S40.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S41.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 11(10P15.3) MUTATED 58 9 4
AMP PEAK 11(10P15.3) WILD-TYPE 114 111 217

Figure S41.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S42.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 11(10P15.3) MUTATED 65 3 0 3
AMP PEAK 11(10P15.3) WILD-TYPE 160 78 167 37

Figure S42.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S43.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 11(10P15.3) MUTATED 41 13 0 16 1
AMP PEAK 11(10P15.3) WILD-TYPE 94 99 108 112 27

Figure S43.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S44.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 11(10P15.3) MUTATED 40 13 0 18
AMP PEAK 11(10P15.3) WILD-TYPE 95 100 125 120

Figure S44.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.049

Table S45.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 11(10P15.3) MUTATED 27 16 21 6
AMP PEAK 11(10P15.3) WILD-TYPE 64 121 167 83

Figure S45.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S46.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 13(12P13.32) MUTATED 46 17 9
AMP PEAK 13(12P13.32) WILD-TYPE 126 103 212

Figure S46.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S47.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 13(12P13.32) MUTATED 55 9 5 3
AMP PEAK 13(12P13.32) WILD-TYPE 170 72 162 37

Figure S47.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.078

Table S48.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 13(12P13.32) MUTATED 30 21 4 13 4
AMP PEAK 13(12P13.32) WILD-TYPE 105 91 104 115 24

Figure S48.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S49.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 13(12P13.32) MUTATED 32 20 5 15
AMP PEAK 13(12P13.32) WILD-TYPE 103 93 120 123

Figure S49.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S50.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 14(12Q14.1) MUTATED 10 22 5
AMP PEAK 14(12Q14.1) WILD-TYPE 162 98 216

Figure S50.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S51.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 14(12Q14.1) MUTATED 13 19 4 1
AMP PEAK 14(12Q14.1) WILD-TYPE 212 62 163 39

Figure S51.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S52.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 14(12Q14.1) MUTATED 3 27 3 3 1
AMP PEAK 14(12Q14.1) WILD-TYPE 132 85 105 125 27

Figure S52.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S53.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 14(12Q14.1) MUTATED 3 26 4 4
AMP PEAK 14(12Q14.1) WILD-TYPE 132 87 121 134

Figure S53.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S54.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 14(12Q14.1) MUTATED 10 5 22
AMP PEAK 14(12Q14.1) WILD-TYPE 212 179 81

Figure S54.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S55.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 14(12Q14.1) MUTATED 6 5 7 19
AMP PEAK 14(12Q14.1) WILD-TYPE 85 132 181 70

Figure S55.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S56.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 16(15Q26.3) MUTATED 12 7 0
AMP PEAK 16(15Q26.3) WILD-TYPE 160 113 221

Figure S56.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S57.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 18(19P13.3) MUTATED 9 40 80
AMP PEAK 18(19P13.3) WILD-TYPE 163 80 141

Figure S57.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S58.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 18(19P13.3) MUTATED 19 27 80 3
AMP PEAK 18(19P13.3) WILD-TYPE 206 54 87 37

Figure S58.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S59.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 18(19P13.3) MUTATED 10 30 56 31 2
AMP PEAK 18(19P13.3) WILD-TYPE 125 82 52 97 26

Figure S59.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S60.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 18(19P13.3) MUTATED 8 31 58 32
AMP PEAK 18(19P13.3) WILD-TYPE 127 82 67 106

Figure S60.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.053

Table S61.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 18(19P13.3) MUTATED 24 23 45 37
AMP PEAK 18(19P13.3) WILD-TYPE 113 84 138 45

Figure S61.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S62.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 19(19P13.2) MUTATED 6 42 74
AMP PEAK 19(19P13.2) WILD-TYPE 166 78 147

Figure S62.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S63.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 19(19P13.2) MUTATED 12 30 77 3
AMP PEAK 19(19P13.2) WILD-TYPE 213 51 90 37

Figure S63.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S64.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 19(19P13.2) MUTATED 6 34 54 25 3
AMP PEAK 19(19P13.2) WILD-TYPE 129 78 54 103 25

Figure S64.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S65.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 19(19P13.2) MUTATED 6 33 57 26
AMP PEAK 19(19P13.2) WILD-TYPE 129 80 68 112

Figure S65.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.098

Table S66.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 19(19P13.2) MUTATED 26 21 39 36
AMP PEAK 19(19P13.2) WILD-TYPE 111 86 144 46

Figure S66.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.22

Table S67.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 19(19P13.2) MUTATED 9 41 43 29
AMP PEAK 19(19P13.2) WILD-TYPE 82 96 145 60

Figure S67.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S68.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 20(XP11.22) MUTATED 33 8 7
AMP PEAK 20(XP11.22) WILD-TYPE 139 112 214

Figure S68.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S69.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 20(XP11.22) MUTATED 41 5 1 1
AMP PEAK 20(XP11.22) WILD-TYPE 184 76 166 39

Figure S69.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.036

Table S70.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 20(XP11.22) MUTATED 22 11 1 14
AMP PEAK 20(XP11.22) WILD-TYPE 113 102 124 124

Figure S70.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S71.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 21(XP11.22) MUTATED 47 7 9
AMP PEAK 21(XP11.22) WILD-TYPE 125 113 212

Figure S71.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S72.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 21(XP11.22) MUTATED 54 6 1 2
AMP PEAK 21(XP11.22) WILD-TYPE 171 75 166 38

Figure S72.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S73.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
AMP PEAK 21(XP11.22) MUTATED 27 17 1 15 3
AMP PEAK 21(XP11.22) WILD-TYPE 108 95 107 113 25

Figure S73.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S74.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
AMP PEAK 21(XP11.22) MUTATED 30 16 1 16
AMP PEAK 21(XP11.22) WILD-TYPE 105 97 124 122

Figure S74.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.14

Table S75.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 21(XP11.22) MUTATED 22 19 20 1
AMP PEAK 21(XP11.22) WILD-TYPE 115 88 163 81

Figure S75.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MRNA_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.19

Table S76.  Gene #22: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 8
DEL PEAK 1(1P36.32) MUTATED 0 8 2
DEL PEAK 1(1P36.32) WILD-TYPE 9 2 6

Figure S76.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.065

Table S77.  Gene #22: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 1(1P36.32) MUTATED 0 1 7 2
DEL PEAK 1(1P36.32) WILD-TYPE 7 6 0 4

Figure S77.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S78.  Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 1(1P36.32) MUTATED 10 29 167
DEL PEAK 1(1P36.32) WILD-TYPE 162 91 54

Figure S78.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S79.  Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 1(1P36.32) MUTATED 11 19 166 10
DEL PEAK 1(1P36.32) WILD-TYPE 214 62 1 30

Figure S79.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S80.  Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 1(1P36.32) MUTATED 5 22 107 58 14
DEL PEAK 1(1P36.32) WILD-TYPE 130 90 1 70 14

Figure S80.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S81.  Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 1(1P36.32) MUTATED 7 21 123 55
DEL PEAK 1(1P36.32) WILD-TYPE 128 92 2 83

Figure S81.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S82.  Gene #22: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 1(1P36.32) MUTATED 33 13 92 68
DEL PEAK 1(1P36.32) WILD-TYPE 104 94 91 14

Figure S82.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S83.  Gene #22: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 1(1P36.32) MUTATED 84 101 21
DEL PEAK 1(1P36.32) WILD-TYPE 138 83 82

Figure S83.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S84.  Gene #22: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 1(1P36.32) MUTATED 44 83 79
DEL PEAK 1(1P36.32) WILD-TYPE 141 78 80

Figure S84.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S85.  Gene #22: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 1(1P36.32) MUTATED 7 83 95 21
DEL PEAK 1(1P36.32) WILD-TYPE 84 54 93 68

Figure S85.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.073

Table S86.  Gene #23: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 2(1P32.3) MUTATED 0 1 7 2
DEL PEAK 2(1P32.3) WILD-TYPE 7 6 0 4

Figure S86.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S87.  Gene #23: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 2(1P32.3) MUTATED 6 24 166
DEL PEAK 2(1P32.3) WILD-TYPE 166 96 55

Figure S87.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S88.  Gene #23: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 2(1P32.3) MUTATED 5 15 166 10
DEL PEAK 2(1P32.3) WILD-TYPE 220 66 1 30

Figure S88.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p32.3' versus 'RPPA_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.23

Table S89.  Gene #23: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
DEL PEAK 2(1P32.3) MUTATED 8 16 28 35
DEL PEAK 2(1P32.3) WILD-TYPE 44 46 40 39

Figure S89.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S90.  Gene #23: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 2(1P32.3) MUTATED 4 17 107 55 13
DEL PEAK 2(1P32.3) WILD-TYPE 131 95 1 73 15

Figure S90.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S91.  Gene #23: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 2(1P32.3) MUTATED 5 17 123 51
DEL PEAK 2(1P32.3) WILD-TYPE 130 96 2 87

Figure S91.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S92.  Gene #23: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 2(1P32.3) MUTATED 33 10 86 67
DEL PEAK 2(1P32.3) WILD-TYPE 104 97 97 15

Figure S92.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S93.  Gene #23: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 2(1P32.3) MUTATED 82 96 18
DEL PEAK 2(1P32.3) WILD-TYPE 140 88 85

Figure S93.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S94.  Gene #23: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 2(1P32.3) MUTATED 39 82 75
DEL PEAK 2(1P32.3) WILD-TYPE 146 79 84

Figure S94.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S95.  Gene #23: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 2(1P32.3) MUTATED 7 82 90 17
DEL PEAK 2(1P32.3) WILD-TYPE 84 55 98 72

Figure S95.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S96.  Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 4(2Q37.3) MUTATED 44 22 11
DEL PEAK 4(2Q37.3) WILD-TYPE 128 98 210

Figure S96.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S97.  Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 4(2Q37.3) MUTATED 64 4 6 3
DEL PEAK 4(2Q37.3) WILD-TYPE 161 77 161 37

Figure S97.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.1

Table S98.  Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 4(2Q37.3) MUTATED 33 22 6 13 3
DEL PEAK 4(2Q37.3) WILD-TYPE 102 90 102 115 25

Figure S98.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S99.  Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 4(2Q37.3) MUTATED 31 23 6 17
DEL PEAK 4(2Q37.3) WILD-TYPE 104 90 119 121

Figure S99.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.065

Table S100.  Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 5(3P21.31) MUTATED 26 15 8
DEL PEAK 5(3P21.31) WILD-TYPE 146 105 213

Figure S100.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.22

Table S101.  Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 5(3P21.31) MUTATED 12 21 8 8
DEL PEAK 5(3P21.31) WILD-TYPE 125 86 175 74

Figure S101.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3q13.31' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.053

Table S102.  Gene #27: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 6(3Q13.31) MUTATED 25 8 6
DEL PEAK 6(3Q13.31) WILD-TYPE 147 112 215

Figure S102.  Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.23

Table S103.  Gene #27: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 6(3Q13.31) MUTATED 16 6 17
DEL PEAK 6(3Q13.31) WILD-TYPE 206 178 86

Figure S103.  Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S104.  Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 7(3Q29) MUTATED 33 10 4
DEL PEAK 7(3Q29) WILD-TYPE 139 110 217

Figure S104.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.18

Table S105.  Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 7(3Q29) MUTATED 31 8 4 4
DEL PEAK 7(3Q29) WILD-TYPE 194 73 163 36

Figure S105.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S106.  Gene #29: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 8(4Q34.3) MUTATED 78 5 51 4
DEL PEAK 8(4Q34.3) WILD-TYPE 147 76 116 36

Figure S106.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S107.  Gene #30: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 9(5P15.33) MUTATED 33 12 5
DEL PEAK 9(5P15.33) WILD-TYPE 139 108 216

Figure S107.  Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S108.  Gene #30: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 9(5P15.33) MUTATED 37 9 3 1
DEL PEAK 9(5P15.33) WILD-TYPE 188 72 164 39

Figure S108.  Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S109.  Gene #31: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 10(5Q34) MUTATED 49 7 8
DEL PEAK 10(5Q34) WILD-TYPE 123 113 213

Figure S109.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S110.  Gene #31: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 10(5Q34) MUTATED 52 7 2 3
DEL PEAK 10(5Q34) WILD-TYPE 173 74 165 37

Figure S110.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.036

Table S111.  Gene #31: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 10(5Q34) MUTATED 19 24 2 13 5
DEL PEAK 10(5Q34) WILD-TYPE 116 88 106 115 23

Figure S111.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S112.  Gene #31: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 10(5Q34) MUTATED 20 25 2 16
DEL PEAK 10(5Q34) WILD-TYPE 115 88 123 122

Figure S112.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q34' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S113.  Gene #31: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 10(5Q34) MUTATED 15 28 18 3
DEL PEAK 10(5Q34) WILD-TYPE 122 79 165 79

Figure S113.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.069

Table S114.  Gene #32: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 11(6P25.3) MUTATED 25 17 8
DEL PEAK 11(6P25.3) WILD-TYPE 147 103 213

Figure S114.  Get High-res Image Gene #32: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S115.  Gene #33: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 12(6Q22.31) MUTATED 29 31 18
DEL PEAK 12(6Q22.31) WILD-TYPE 143 89 203

Figure S115.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S116.  Gene #33: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 12(6Q22.31) MUTATED 49 16 8 5
DEL PEAK 12(6Q22.31) WILD-TYPE 176 65 159 35

Figure S116.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.22

Table S117.  Gene #33: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 12(6Q22.31) MUTATED 27 25 7 18
DEL PEAK 12(6Q22.31) WILD-TYPE 108 88 118 120

Figure S117.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S118.  Gene #33: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 12(6Q22.31) MUTATED 24 11 18 22
DEL PEAK 12(6Q22.31) WILD-TYPE 67 126 170 67

Figure S118.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q24.3' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S119.  Gene #34: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 13(6Q24.3) MUTATED 32 30 20
DEL PEAK 13(6Q24.3) WILD-TYPE 140 90 201

Figure S119.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S120.  Gene #34: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 13(6Q24.3) MUTATED 53 16 8 5
DEL PEAK 13(6Q24.3) WILD-TYPE 172 65 159 35

Figure S120.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.04

Table S121.  Gene #34: 'del_6q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 13(6Q24.3) MUTATED 31 25 7 18
DEL PEAK 13(6Q24.3) WILD-TYPE 104 88 118 120

Figure S121.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.057

Table S122.  Gene #34: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 13(6Q24.3) MUTATED 36 20 20 5
DEL PEAK 13(6Q24.3) WILD-TYPE 101 87 163 77

Figure S122.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S123.  Gene #34: 'del_6q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 13(6Q24.3) MUTATED 27 12 19 21
DEL PEAK 13(6Q24.3) WILD-TYPE 64 125 169 68

Figure S123.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S124.  Gene #36: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 15(8Q24.3) MUTATED 15 13 1
DEL PEAK 15(8Q24.3) WILD-TYPE 157 107 220

Figure S124.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S125.  Gene #36: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 15(8Q24.3) MUTATED 17 11 0 1
DEL PEAK 15(8Q24.3) WILD-TYPE 208 70 167 39

Figure S125.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.24

Table S126.  Gene #36: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 15(8Q24.3) MUTATED 10 12 0 7
DEL PEAK 15(8Q24.3) WILD-TYPE 125 101 125 131

Figure S126.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S127.  Gene #37: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 16(9P23) MUTATED 55 57 38
DEL PEAK 16(9P23) WILD-TYPE 117 63 183

Figure S127.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S128.  Gene #37: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 16(9P23) MUTATED 79 35 28 8
DEL PEAK 16(9P23) WILD-TYPE 146 46 139 32

Figure S128.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S129.  Gene #38: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 17(9P21.3) MUTATED 63 77 36
DEL PEAK 17(9P21.3) WILD-TYPE 109 43 185

Figure S129.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S130.  Gene #38: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 17(9P21.3) MUTATED 82 59 27 8
DEL PEAK 17(9P21.3) WILD-TYPE 143 22 140 32

Figure S130.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S131.  Gene #38: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
DEL PEAK 17(9P21.3) MUTATED 12 38 26 18
DEL PEAK 17(9P21.3) WILD-TYPE 40 24 42 56

Figure S131.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S132.  Gene #38: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 131 58
DEL PEAK 17(9P21.3) MUTATED 11 65 18
DEL PEAK 17(9P21.3) WILD-TYPE 56 66 40

Figure S132.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S133.  Gene #38: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 17(9P21.3) MUTATED 40 66 19 44 7
DEL PEAK 17(9P21.3) WILD-TYPE 95 46 89 84 21

Figure S133.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S134.  Gene #38: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 17(9P21.3) MUTATED 44 65 23 44
DEL PEAK 17(9P21.3) WILD-TYPE 91 48 102 94

Figure S134.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S135.  Gene #38: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 17(9P21.3) MUTATED 59 56 60
DEL PEAK 17(9P21.3) WILD-TYPE 163 128 43

Figure S135.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S136.  Gene #38: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 17(9P21.3) MUTATED 31 28 54 61
DEL PEAK 17(9P21.3) WILD-TYPE 60 109 134 28

Figure S136.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S137.  Gene #39: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 18(10Q26.3) MUTATED 53 85 13
DEL PEAK 18(10Q26.3) WILD-TYPE 119 35 208

Figure S137.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S138.  Gene #39: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 18(10Q26.3) MUTATED 64 72 8 7
DEL PEAK 18(10Q26.3) WILD-TYPE 161 9 159 33

Figure S138.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S139.  Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
DEL PEAK 18(10Q26.3) MUTATED 13 35 14 11
DEL PEAK 18(10Q26.3) WILD-TYPE 39 27 54 63

Figure S139.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.11

Table S140.  Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 131 58
DEL PEAK 18(10Q26.3) MUTATED 11 52 10
DEL PEAK 18(10Q26.3) WILD-TYPE 56 79 48

Figure S140.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S141.  Gene #39: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 18(10Q26.3) MUTATED 32 81 4 26 7
DEL PEAK 18(10Q26.3) WILD-TYPE 103 31 104 102 21

Figure S141.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S142.  Gene #39: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 18(10Q26.3) MUTATED 34 81 8 27
DEL PEAK 18(10Q26.3) WILD-TYPE 101 32 117 111

Figure S142.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S143.  Gene #39: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 18(10Q26.3) MUTATED 55 46 39 11
DEL PEAK 18(10Q26.3) WILD-TYPE 82 61 144 71

Figure S143.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S144.  Gene #39: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 18(10Q26.3) MUTATED 49 28 74
DEL PEAK 18(10Q26.3) WILD-TYPE 173 156 29

Figure S144.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S145.  Gene #39: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 18(10Q26.3) MUTATED 94 22 35
DEL PEAK 18(10Q26.3) WILD-TYPE 91 139 124

Figure S145.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S146.  Gene #39: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 18(10Q26.3) MUTATED 28 18 33 72
DEL PEAK 18(10Q26.3) WILD-TYPE 63 119 155 17

Figure S146.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.21

Table S147.  Gene #40: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 19(11P15.5) MUTATED 1 6 0 0
DEL PEAK 19(11P15.5) WILD-TYPE 6 1 7 6

Figure S147.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S148.  Gene #40: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 19(11P15.5) MUTATED 74 20 10
DEL PEAK 19(11P15.5) WILD-TYPE 98 100 211

Figure S148.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S149.  Gene #40: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 19(11P15.5) MUTATED 85 14 0 5
DEL PEAK 19(11P15.5) WILD-TYPE 140 67 167 35

Figure S149.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S150.  Gene #40: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 19(11P15.5) MUTATED 39 35 0 23 6
DEL PEAK 19(11P15.5) WILD-TYPE 96 77 108 105 22

Figure S150.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S151.  Gene #40: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 19(11P15.5) MUTATED 38 38 0 27
DEL PEAK 19(11P15.5) WILD-TYPE 97 75 125 111

Figure S151.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S152.  Gene #40: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 19(11P15.5) MUTATED 23 40 33 8
DEL PEAK 19(11P15.5) WILD-TYPE 114 67 150 74

Figure S152.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S153.  Gene #41: 'del_11p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 20(11P15.1) MUTATED 52 15 5
DEL PEAK 20(11P15.1) WILD-TYPE 120 105 216

Figure S153.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S154.  Gene #41: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 20(11P15.1) MUTATED 52 14 1 5
DEL PEAK 20(11P15.1) WILD-TYPE 173 67 166 35

Figure S154.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S155.  Gene #41: 'del_11p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 20(11P15.1) MUTATED 17 35 1 12 6
DEL PEAK 20(11P15.1) WILD-TYPE 118 77 107 116 22

Figure S155.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S156.  Gene #41: 'del_11p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 20(11P15.1) MUTATED 20 38 1 12
DEL PEAK 20(11P15.1) WILD-TYPE 115 75 124 126

Figure S156.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S157.  Gene #41: 'del_11p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 20(11P15.1) MUTATED 16 32 19 5
DEL PEAK 20(11P15.1) WILD-TYPE 121 75 164 77

Figure S157.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S158.  Gene #41: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 20(11P15.1) MUTATED 27 16 29
DEL PEAK 20(11P15.1) WILD-TYPE 195 168 74

Figure S158.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S159.  Gene #43: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 22(12Q12) MUTATED 53 7 12
DEL PEAK 22(12Q12) WILD-TYPE 119 113 209

Figure S159.  Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S160.  Gene #43: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 22(12Q12) MUTATED 57 5 8 2
DEL PEAK 22(12Q12) WILD-TYPE 168 76 159 38

Figure S160.  Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S161.  Gene #44: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 23(13Q14.2) MUTATED 2 7 0 0
DEL PEAK 23(13Q14.2) WILD-TYPE 5 0 7 6

Figure S161.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S162.  Gene #44: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 23(13Q14.2) MUTATED 73 36 33
DEL PEAK 23(13Q14.2) WILD-TYPE 99 84 188

Figure S162.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S163.  Gene #44: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 23(13Q14.2) MUTATED 80 28 27 7
DEL PEAK 23(13Q14.2) WILD-TYPE 145 53 140 33

Figure S163.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.086

Table S164.  Gene #44: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 23(13Q14.2) MUTATED 40 47 16 32 7
DEL PEAK 23(13Q14.2) WILD-TYPE 95 65 92 96 21

Figure S164.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0094

Table S165.  Gene #44: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 23(13Q14.2) MUTATED 43 47 19 33
DEL PEAK 23(13Q14.2) WILD-TYPE 92 66 106 105

Figure S165.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S166.  Gene #45: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 24(13Q14.2) MUTATED 2 7 0 0
DEL PEAK 24(13Q14.2) WILD-TYPE 5 0 7 6

Figure S166.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S167.  Gene #45: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 24(13Q14.2) MUTATED 74 37 33
DEL PEAK 24(13Q14.2) WILD-TYPE 98 83 188

Figure S167.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S168.  Gene #45: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 24(13Q14.2) MUTATED 81 29 27 7
DEL PEAK 24(13Q14.2) WILD-TYPE 144 52 140 33

Figure S168.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.061

Table S169.  Gene #45: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 24(13Q14.2) MUTATED 41 48 16 32 7
DEL PEAK 24(13Q14.2) WILD-TYPE 94 64 92 96 21

Figure S169.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S170.  Gene #45: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 24(13Q14.2) MUTATED 44 48 19 33
DEL PEAK 24(13Q14.2) WILD-TYPE 91 65 106 105

Figure S170.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.044

Table S171.  Gene #46: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 25(13Q34) MUTATED 52 30 28
DEL PEAK 25(13Q34) WILD-TYPE 120 90 193

Figure S171.  Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.22

Table S172.  Gene #47: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 26(14Q24.3) MUTATED 25 44 23 21 7
DEL PEAK 26(14Q24.3) WILD-TYPE 110 68 85 107 21

Figure S172.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.04

Table S173.  Gene #47: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 26(14Q24.3) MUTATED 32 44 24 20
DEL PEAK 26(14Q24.3) WILD-TYPE 103 69 101 118

Figure S173.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.13

Table S174.  Gene #47: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 26(14Q24.3) MUTATED 51 21 32 16
DEL PEAK 26(14Q24.3) WILD-TYPE 86 86 151 66

Figure S174.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S175.  Gene #49: 'del_19q13.41' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 28(19Q13.41) MUTATED 40 35 192
DEL PEAK 28(19Q13.41) WILD-TYPE 132 85 29

Figure S175.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.41' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S176.  Gene #49: 'del_19q13.41' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 28(19Q13.41) MUTATED 78 12 167 10
DEL PEAK 28(19Q13.41) WILD-TYPE 147 69 0 30

Figure S176.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.41' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S177.  Gene #49: 'del_19q13.41' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 28(19Q13.41) MUTATED 40 33 108 73 12
DEL PEAK 28(19Q13.41) WILD-TYPE 95 79 0 55 16

Figure S177.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.41' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S178.  Gene #49: 'del_19q13.41' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 28(19Q13.41) MUTATED 39 31 124 72
DEL PEAK 28(19Q13.41) WILD-TYPE 96 82 1 66

Figure S178.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S179.  Gene #49: 'del_19q13.41' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 28(19Q13.41) MUTATED 50 36 107 74
DEL PEAK 28(19Q13.41) WILD-TYPE 87 71 76 8

Figure S179.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.41' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S180.  Gene #49: 'del_19q13.41' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 28(19Q13.41) MUTATED 129 118 20
DEL PEAK 28(19Q13.41) WILD-TYPE 93 66 83

Figure S180.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S181.  Gene #49: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 28(19Q13.41) MUTATED 61 110 95
DEL PEAK 28(19Q13.41) WILD-TYPE 124 51 64

Figure S181.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.41' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S182.  Gene #49: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 28(19Q13.41) MUTATED 32 105 113 16
DEL PEAK 28(19Q13.41) WILD-TYPE 59 32 75 73

Figure S182.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S183.  Gene #50: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 29(19Q13.42) MUTATED 42 38 198
DEL PEAK 29(19Q13.42) WILD-TYPE 130 82 23

Figure S183.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S184.  Gene #50: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 29(19Q13.42) MUTATED 88 13 167 10
DEL PEAK 29(19Q13.42) WILD-TYPE 137 68 0 30

Figure S184.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.42' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S185.  Gene #50: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 29(19Q13.42) MUTATED 49 35 108 73 12
DEL PEAK 29(19Q13.42) WILD-TYPE 86 77 0 55 16

Figure S185.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S186.  Gene #50: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 29(19Q13.42) MUTATED 46 33 124 74
DEL PEAK 29(19Q13.42) WILD-TYPE 89 80 1 64

Figure S186.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S187.  Gene #50: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 29(19Q13.42) MUTATED 56 40 106 76
DEL PEAK 29(19Q13.42) WILD-TYPE 81 67 77 6

Figure S187.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S188.  Gene #50: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 29(19Q13.42) MUTATED 137 119 22
DEL PEAK 29(19Q13.42) WILD-TYPE 85 65 81

Figure S188.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S189.  Gene #50: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 29(19Q13.42) MUTATED 69 113 95
DEL PEAK 29(19Q13.42) WILD-TYPE 116 48 64

Figure S189.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.42' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S190.  Gene #50: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 29(19Q13.42) MUTATED 36 109 115 17
DEL PEAK 29(19Q13.42) WILD-TYPE 55 28 73 72

Figure S190.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S191.  Gene #51: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 30(22Q13.31) MUTATED 34 35 8
DEL PEAK 30(22Q13.31) WILD-TYPE 138 85 213

Figure S191.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S192.  Gene #51: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 30(22Q13.31) MUTATED 39 29 4 5
DEL PEAK 30(22Q13.31) WILD-TYPE 186 52 163 35

Figure S192.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.12

Table S193.  Gene #51: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 62 68 74
DEL PEAK 30(22Q13.31) MUTATED 4 21 8 6
DEL PEAK 30(22Q13.31) WILD-TYPE 48 41 60 68

Figure S193.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S194.  Gene #51: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 135 112 108 128 28
DEL PEAK 30(22Q13.31) MUTATED 15 40 2 14 5
DEL PEAK 30(22Q13.31) WILD-TYPE 120 72 106 114 23

Figure S194.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S195.  Gene #51: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 125 138
DEL PEAK 30(22Q13.31) MUTATED 17 39 4 16
DEL PEAK 30(22Q13.31) WILD-TYPE 118 74 121 122

Figure S195.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S196.  Gene #51: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 30(22Q13.31) MUTATED 27 18 32
DEL PEAK 30(22Q13.31) WILD-TYPE 195 166 71

Figure S196.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S197.  Gene #51: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 30(22Q13.31) MUTATED 11 18 18 29
DEL PEAK 30(22Q13.31) WILD-TYPE 80 119 170 60

Figure S197.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 513

  • Number of significantly focal cnvs = 52

  • 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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)