Correlation between copy number variations of arm-level result and molecular subtypes
Esophageal Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
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 (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C10K27Z4
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 184 patients, 250 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF'.

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

  • 4q gain cnv correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 9p gain cnv correlated to 'MIRSEQ_CNMF'.

  • 9q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'CN_CNMF'.

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

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'MIRSEQ_CNMF'.

  • 18q gain cnv correlated to 'MIRSEQ_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF'.

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

  • 22q gain 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'.

  • xq gain cnv correlated to 'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 1q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 2p loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 7q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

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

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

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

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 14q loss 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'.

  • 15q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q loss 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'.

  • 17p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • xp loss cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CNMF'.

  • xq loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  '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 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 250 significant findings detected.

Clinical
Features
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
22q gain 31 (17%) 153 1e-05
(0.000586)
3e-05
(0.00082)
0.00411
(0.0296)
0.00054
(0.00692)
1e-05
(0.000586)
3e-05
(0.00082)
0.0002
(0.00315)
1e-05
(0.000586)
1e-05
(0.000586)
3e-05
(0.00082)
14q loss 45 (24%) 139 1e-05
(0.000586)
0.0198
(0.0918)
0.00407
(0.0295)
0.00289
(0.0239)
0.00442
(0.0307)
0.0187
(0.088)
0.0169
(0.0817)
0.00283
(0.0237)
0.0419
(0.144)
0.00251
(0.0216)
16q loss 53 (29%) 131 5e-05
(0.00117)
0.00048
(0.00635)
0.0368
(0.132)
0.0288
(0.115)
0.00046
(0.00618)
2e-05
(0.000745)
0.00016
(0.00262)
2e-05
(0.000745)
2e-05
(0.000745)
1e-05
(0.000586)
12p loss 34 (18%) 150 0.0229
(0.101)
0.0297
(0.115)
0.151
(0.318)
0.0323
(0.122)
0.00993
(0.0554)
0.00167
(0.0159)
0.0265
(0.109)
0.00381
(0.0284)
0.0426
(0.146)
0.00056
(0.00696)
22q loss 73 (40%) 111 2e-05
(0.000745)
0.0009
(0.00971)
0.0131
(0.0686)
0.082
(0.225)
0.00012
(0.00214)
6e-05
(0.00133)
0.00709
(0.0427)
0.00016
(0.00262)
1e-05
(0.000586)
1e-05
(0.000586)
13q gain 44 (24%) 140 0.00011
(0.00205)
0.00117
(0.0118)
0.221
(0.409)
0.112
(0.273)
0.0001
(0.00191)
2e-05
(0.000745)
3e-05
(0.00082)
5e-05
(0.00117)
5e-05
(0.00117)
1e-05
(0.000586)
20q gain 114 (62%) 70 3e-05
(0.00082)
0.00194
(0.0179)
0.151
(0.318)
0.119
(0.279)
0.00253
(0.0216)
0.00399
(0.0292)
0.00113
(0.0116)
0.00245
(0.0216)
0.0227
(0.101)
0.0002
(0.00315)
3p loss 92 (50%) 92 3e-05
(0.00082)
0.00016
(0.00262)
0.167
(0.339)
0.0859
(0.228)
0.00058
(0.0071)
1e-05
(0.000586)
0.00136
(0.0134)
3e-05
(0.00082)
0.00107
(0.0112)
1e-05
(0.000586)
5p loss 46 (25%) 138 0.0048
(0.0324)
0.00083
(0.00932)
0.388
(0.595)
0.0522
(0.167)
4e-05
(0.00106)
0.0001
(0.00191)
2e-05
(0.000745)
3e-05
(0.00082)
8e-05
(0.00168)
1e-05
(0.000586)
10p loss 51 (28%) 133 0.00147
(0.0142)
0.00373
(0.0281)
0.119
(0.279)
0.383
(0.591)
0.00725
(0.0429)
0.00977
(0.0549)
0.024
(0.104)
0.00572
(0.0361)
0.0151
(0.0764)
0.00258
(0.0218)
10q loss 50 (27%) 134 7e-05
(0.00151)
6e-05
(0.00133)
0.666
(0.811)
0.105
(0.26)
0.0053
(0.0342)
0.00131
(0.0131)
0.0242
(0.104)
0.00184
(0.0173)
0.00651
(0.0401)
0.00108
(0.0112)
16p loss 54 (29%) 130 0.00075
(0.00866)
0.00728
(0.0429)
0.719
(0.841)
0.685
(0.82)
0.00322
(0.0261)
0.0001
(0.00191)
0.00675
(0.0413)
0.00024
(0.00358)
0.00042
(0.00574)
0.00026
(0.00381)
17p loss 72 (39%) 112 0.00012
(0.00214)
0.00071
(0.00832)
0.229
(0.421)
0.303
(0.497)
0.0157
(0.0783)
0.00143
(0.014)
0.00455
(0.0314)
0.00209
(0.019)
0.0452
(0.151)
0.00024
(0.00358)
18p loss 69 (38%) 115 2e-05
(0.000745)
0.018
(0.0859)
0.235
(0.428)
0.697
(0.828)
0.017
(0.0817)
0.00395
(0.0292)
0.00368
(0.0281)
0.0199
(0.0918)
0.00878
(0.0503)
0.00566
(0.036)
18q loss 103 (56%) 81 5e-05
(0.00117)
0.0296
(0.115)
0.425
(0.632)
0.846
(0.92)
0.00528
(0.0342)
0.0191
(0.0895)
0.00244
(0.0216)
0.00028
(0.00403)
0.0435
(0.148)
0.00016
(0.00262)
12p gain 57 (31%) 127 0.00041
(0.0057)
0.00233
(0.021)
0.457
(0.654)
0.0929
(0.239)
0.00341
(0.0269)
0.00541
(0.0347)
0.101
(0.254)
0.0025
(0.0216)
0.00876
(0.0503)
0.0124
(0.0658)
1p loss 38 (21%) 146 0.00088
(0.00962)
2e-05
(0.000745)
0.858
(0.923)
0.917
(0.956)
0.00093
(0.0099)
0.0375
(0.133)
0.0936
(0.24)
0.031
(0.119)
0.0166
(0.0815)
0.026
(0.108)
5p gain 75 (41%) 109 0.0004
(0.00566)
0.00365
(0.0281)
0.414
(0.623)
0.0919
(0.237)
0.0359
(0.131)
0.017
(0.0817)
0.171
(0.344)
0.0399
(0.14)
0.0811
(0.224)
0.00771
(0.0452)
14q gain 49 (27%) 135 0.0247
(0.105)
0.295
(0.489)
0.0144
(0.0735)
0.157
(0.326)
0.179
(0.356)
0.0157
(0.0783)
0.071
(0.205)
0.034
(0.126)
0.0162
(0.0798)
0.0417
(0.144)
16q gain 38 (21%) 146 0.00422
(0.0298)
0.0481
(0.159)
0.0871
(0.23)
0.0245
(0.105)
0.0741
(0.21)
0.0435
(0.148)
0.149
(0.317)
0.0291
(0.115)
0.0222
(0.0996)
0.0636
(0.19)
16p gain 40 (22%) 144 0.0135
(0.0696)
0.0369
(0.132)
0.199
(0.384)
0.185
(0.364)
0.142
(0.308)
0.00502
(0.0332)
0.167
(0.339)
0.0373
(0.133)
0.0488
(0.161)
0.108
(0.265)
xq gain 41 (22%) 143 0.0503
(0.164)
0.268
(0.457)
0.0358
(0.131)
0.082
(0.225)
0.0273
(0.111)
0.0264
(0.109)
0.23
(0.422)
0.0311
(0.119)
0.0473
(0.157)
0.0504
(0.164)
12q loss 32 (17%) 152 0.0692
(0.202)
0.0364
(0.131)
0.216
(0.405)
0.0542
(0.171)
0.0626
(0.188)
0.0112
(0.0605)
0.12
(0.279)
0.0417
(0.144)
0.0278
(0.112)
0.0103
(0.057)
xq loss 39 (21%) 145 0.29
(0.482)
0.085
(0.227)
0.0001
(0.00191)
0.0261
(0.108)
0.0105
(0.0576)
0.0511
(0.165)
0.0656
(0.194)
0.00295
(0.0242)
0.0918
(0.237)
0.0134
(0.0696)
2p gain 61 (33%) 123 0.00336
(0.0267)
0.00065
(0.00784)
0.258
(0.448)
0.215
(0.404)
0.0249
(0.105)
0.0911
(0.236)
0.0614
(0.185)
0.34
(0.54)
0.0236
(0.103)
0.674
(0.814)
6p gain 39 (21%) 145 0.134
(0.297)
0.511
(0.71)
0.0804
(0.224)
0.0543
(0.171)
0.352
(0.555)
0.12
(0.279)
0.0293
(0.115)
0.0226
(0.101)
0.0185
(0.0878)
0.0109
(0.0591)
4p loss 105 (57%) 79 0.00085
(0.00942)
0.00416
(0.0297)
0.242
(0.433)
0.94
(0.968)
0.0333
(0.125)
0.212
(0.403)
0.771
(0.88)
0.285
(0.478)
0.0194
(0.0905)
0.171
(0.344)
11q loss 60 (33%) 124 0.00053
(0.0069)
0.0222
(0.0996)
0.928
(0.961)
0.746
(0.864)
0.00584
(0.0363)
0.0285
(0.115)
0.454
(0.653)
0.143
(0.308)
0.141
(0.307)
0.0844
(0.227)
10q gain 31 (17%) 153 0.00372
(0.0281)
0.0141
(0.0721)
0.923
(0.96)
0.831
(0.912)
0.0727
(0.209)
0.116
(0.277)
0.163
(0.335)
0.0999
(0.253)
0.218
(0.406)
0.0321
(0.122)
2q loss 18 (10%) 166 0.544
(0.735)
0.239
(0.431)
0.849
(0.923)
0.422
(0.63)
0.0131
(0.0686)
0.0325
(0.122)
0.113
(0.273)
0.0072
(0.0429)
0.282
(0.474)
0.105
(0.26)
5q loss 87 (47%) 97 0.00186
(0.0173)
0.00022
(0.0034)
0.33
(0.529)
0.133
(0.297)
0.00482
(0.0324)
0.136
(0.299)
0.103
(0.256)
0.134
(0.297)
0.0877
(0.23)
0.0846
(0.227)
9q loss 65 (35%) 119 0.017
(0.0817)
0.0249
(0.105)
0.791
(0.888)
0.261
(0.448)
0.0298
(0.115)
0.423
(0.63)
0.0843
(0.227)
0.344
(0.544)
0.215
(0.404)
0.608
(0.768)
13q loss 67 (36%) 117 0.00326
(0.0262)
0.0731
(0.21)
0.782
(0.884)
0.662
(0.808)
0.15
(0.318)
0.0336
(0.125)
0.215
(0.404)
0.15
(0.318)
0.0375
(0.133)
0.0997
(0.253)
15q loss 56 (30%) 128 0.0563
(0.176)
0.134
(0.297)
0.204
(0.392)
0.254
(0.447)
0.0594
(0.181)
0.0363
(0.131)
0.551
(0.74)
0.00432
(0.0303)
0.305
(0.498)
0.00055
(0.00694)
2q gain 47 (26%) 137 0.00955
(0.054)
0.0306
(0.118)
0.117
(0.277)
0.444
(0.648)
0.0834
(0.226)
0.103
(0.256)
0.554
(0.741)
0.906
(0.951)
0.41
(0.62)
0.527
(0.722)
3q gain 77 (42%) 107 1e-05
(0.000586)
0.00528
(0.0342)
0.6
(0.765)
0.257
(0.448)
0.676
(0.814)
0.0825
(0.225)
0.817
(0.903)
0.238
(0.43)
0.114
(0.275)
0.334
(0.534)
4q gain 17 (9%) 167 0.261
(0.448)
0.622
(0.778)
0.00355
(0.0277)
0.0047
(0.0321)
0.145
(0.312)
0.163
(0.335)
0.927
(0.961)
0.744
(0.864)
0.694
(0.826)
0.447
(0.648)
10p gain 40 (22%) 144 0.00584
(0.0363)
0.0645
(0.192)
0.353
(0.555)
0.458
(0.655)
0.164
(0.336)
0.0791
(0.221)
0.0388
(0.136)
0.215
(0.404)
0.183
(0.362)
0.0752
(0.212)
1q loss 22 (12%) 162 0.0494
(0.162)
0.14
(0.306)
0.136
(0.299)
0.584
(0.76)
0.256
(0.448)
0.0508
(0.165)
0.0294
(0.115)
0.121
(0.281)
0.0709
(0.205)
0.0756
(0.212)
2p loss 10 (5%) 174 0.571
(0.753)
0.0554
(0.174)
0.201
(0.386)
0.0683
(0.2)
0.0105
(0.0576)
0.152
(0.318)
0.183
(0.362)
0.0008
(0.00911)
0.56
(0.747)
0.19
(0.371)
4q loss 88 (48%) 96 1e-05
(0.000586)
0.00903
(0.0514)
0.124
(0.284)
0.713
(0.837)
0.123
(0.284)
0.192
(0.375)
0.445
(0.648)
0.448
(0.648)
0.1
(0.253)
0.115
(0.277)
9p loss 100 (54%) 84 0.0217
(0.0984)
0.455
(0.653)
0.895
(0.947)
0.69
(0.824)
0.0204
(0.0928)
0.232
(0.424)
0.503
(0.702)
0.812
(0.9)
0.871
(0.929)
0.646
(0.803)
19q loss 52 (28%) 132 0.0422
(0.145)
0.356
(0.559)
0.0811
(0.224)
0.381
(0.589)
0.223
(0.411)
0.0274
(0.111)
0.493
(0.691)
0.536
(0.729)
0.0532
(0.17)
0.282
(0.474)
21q loss 108 (59%) 76 0.007
(0.0425)
0.00855
(0.0497)
0.26
(0.448)
0.0894
(0.233)
0.103
(0.256)
0.101
(0.254)
0.136
(0.299)
0.221
(0.409)
0.125
(0.286)
0.0878
(0.23)
xp loss 60 (33%) 124 0.243
(0.434)
0.656
(0.807)
0.0439
(0.148)
0.343
(0.543)
0.0267
(0.109)
0.809
(0.9)
0.815
(0.902)
0.244
(0.434)
0.601
(0.765)
0.265
(0.452)
1q gain 64 (35%) 120 0.0114
(0.0609)
0.108
(0.264)
0.296
(0.489)
0.0539
(0.171)
0.162
(0.334)
0.579
(0.76)
0.583
(0.76)
0.654
(0.806)
0.589
(0.761)
0.787
(0.885)
3p gain 31 (17%) 153 0.00491
(0.0327)
0.257
(0.448)
0.835
(0.914)
0.758
(0.875)
0.596
(0.765)
0.308
(0.499)
0.786
(0.885)
0.608
(0.768)
0.924
(0.96)
0.662
(0.808)
7q gain 87 (47%) 97 0.0351
(0.129)
0.167
(0.339)
0.718
(0.841)
0.524
(0.72)
0.462
(0.659)
0.466
(0.662)
0.413
(0.623)
0.687
(0.821)
0.859
(0.923)
0.321
(0.517)
9p gain 17 (9%) 167 0.0743
(0.21)
0.058
(0.179)
0.619
(0.776)
0.135
(0.297)
0.671
(0.814)
0.658
(0.807)
0.0407
(0.142)
0.278
(0.471)
0.809
(0.9)
0.566
(0.749)
9q gain 34 (18%) 150 0.142
(0.308)
0.064
(0.191)
0.159
(0.33)
0.455
(0.653)
0.24
(0.431)
0.536
(0.729)
0.213
(0.404)
0.0204
(0.0928)
0.244
(0.434)
0.0611
(0.185)
11p gain 39 (21%) 145 0.0451
(0.151)
0.0649
(0.192)
0.997
(1.00)
0.838
(0.915)
0.575
(0.757)
0.783
(0.884)
0.214
(0.404)
0.318
(0.513)
0.679
(0.814)
0.704
(0.831)
12q gain 37 (20%) 147 0.0297
(0.115)
0.782
(0.884)
0.952
(0.973)
0.561
(0.747)
0.402
(0.611)
0.693
(0.826)
0.75
(0.866)
0.608
(0.768)
0.248
(0.44)
0.418
(0.627)
17p gain 32 (17%) 152 0.0158
(0.0787)
0.702
(0.831)
0.658
(0.807)
0.598
(0.765)
0.0587
(0.181)
0.0592
(0.181)
0.287
(0.48)
0.588
(0.761)
0.252
(0.444)
0.472
(0.667)
18p gain 50 (27%) 134 0.128
(0.29)
0.599
(0.765)
0.303
(0.497)
0.768
(0.878)
0.328
(0.527)
0.336
(0.534)
0.025
(0.105)
0.871
(0.929)
0.741
(0.863)
0.803
(0.9)
18q gain 24 (13%) 160 1
(1.00)
0.844
(0.92)
0.584
(0.76)
0.335
(0.534)
0.17
(0.342)
0.86
(0.923)
0.0113
(0.0605)
0.11
(0.268)
0.929
(0.961)
0.165
(0.337)
20p gain 107 (58%) 77 0.0007
(0.00832)
0.187
(0.367)
0.488
(0.686)
0.252
(0.444)
0.519
(0.718)
0.261
(0.448)
0.124
(0.284)
0.353
(0.555)
0.523
(0.72)
0.0734
(0.21)
7q loss 23 (12%) 161 0.204
(0.391)
0.124
(0.284)
0.706
(0.832)
0.208
(0.398)
0.0341
(0.126)
0.587
(0.761)
0.76
(0.876)
0.966
(0.983)
0.391
(0.598)
1
(1.00)
8p loss 62 (34%) 122 0.0239
(0.104)
0.609
(0.769)
0.553
(0.741)
0.972
(0.987)
0.465
(0.661)
0.71
(0.835)
0.529
(0.725)
0.805
(0.9)
0.82
(0.905)
0.587
(0.761)
19p loss 64 (35%) 120 0.147
(0.315)
0.178
(0.354)
0.197
(0.382)
0.856
(0.923)
0.0986
(0.251)
0.564
(0.748)
0.435
(0.641)
0.385
(0.592)
0.371
(0.578)
0.046
(0.153)
1p gain 38 (21%) 146 0.199
(0.384)
0.781
(0.884)
0.305
(0.498)
0.19
(0.371)
0.235
(0.428)
0.601
(0.765)
0.307
(0.499)
0.855
(0.923)
0.744
(0.864)
0.852
(0.923)
4p gain 17 (9%) 167 0.0976
(0.249)
0.36
(0.563)
0.195
(0.379)
0.17
(0.342)
0.453
(0.653)
0.533
(0.729)
0.967
(0.983)
1
(1.00)
0.811
(0.9)
1
(1.00)
5q gain 20 (11%) 164 0.443
(0.648)
0.658
(0.807)
0.493
(0.691)
0.549
(0.739)
0.779
(0.884)
0.836
(0.914)
0.928
(0.961)
0.948
(0.972)
0.7
(0.83)
0.81
(0.9)
6q gain 33 (18%) 151 0.129
(0.291)
0.523
(0.72)
0.0767
(0.215)
0.113
(0.273)
0.411
(0.62)
0.153
(0.32)
0.13
(0.293)
0.166
(0.339)
0.0573
(0.178)
0.0663
(0.195)
7p gain 109 (59%) 75 0.0699
(0.203)
0.437
(0.641)
0.305
(0.498)
0.302
(0.497)
0.237
(0.429)
0.262
(0.449)
0.7
(0.83)
0.274
(0.464)
0.437
(0.641)
0.148
(0.315)
8p gain 67 (36%) 117 0.626
(0.782)
0.982
(0.995)
0.889
(0.942)
0.869
(0.929)
0.718
(0.841)
0.088
(0.23)
0.0851
(0.227)
0.777
(0.884)
0.765
(0.878)
0.739
(0.862)
8q gain 102 (55%) 82 0.87
(0.929)
0.854
(0.923)
0.448
(0.648)
0.177
(0.354)
0.776
(0.884)
0.373
(0.58)
0.875
(0.93)
0.607
(0.768)
0.766
(0.878)
1
(1.00)
11q gain 29 (16%) 155 0.117
(0.277)
0.374
(0.58)
0.903
(0.95)
0.951
(0.973)
0.545
(0.736)
0.218
(0.406)
0.268
(0.457)
0.338
(0.537)
0.127
(0.289)
0.188
(0.369)
15q gain 31 (17%) 153 0.178
(0.354)
0.523
(0.72)
0.429
(0.636)
0.237
(0.43)
0.404
(0.613)
0.0741
(0.21)
0.399
(0.609)
0.54
(0.731)
0.313
(0.508)
0.552
(0.74)
17q gain 44 (24%) 140 0.405
(0.613)
0.673
(0.814)
0.997
(1.00)
0.745
(0.864)
0.322
(0.518)
0.059
(0.181)
0.422
(0.63)
0.962
(0.981)
0.809
(0.9)
0.833
(0.913)
19p gain 28 (15%) 156 0.509
(0.71)
0.158
(0.329)
0.536
(0.729)
0.481
(0.678)
0.396
(0.605)
0.875
(0.93)
0.429
(0.636)
0.826
(0.909)
0.653
(0.806)
0.882
(0.936)
19q gain 40 (22%) 144 0.362
(0.565)
0.432
(0.638)
0.515
(0.713)
0.116
(0.277)
0.452
(0.652)
0.295
(0.489)
0.0613
(0.185)
0.588
(0.761)
0.539
(0.731)
0.211
(0.403)
21q gain 16 (9%) 168 0.511
(0.71)
0.0514
(0.165)
0.664
(0.81)
0.619
(0.776)
0.153
(0.319)
0.26
(0.448)
0.0882
(0.23)
0.445
(0.648)
0.59
(0.761)
0.617
(0.776)
xp gain 25 (14%) 159 0.583
(0.76)
0.26
(0.448)
0.235
(0.428)
0.115
(0.277)
0.648
(0.804)
0.704
(0.831)
0.244
(0.434)
0.122
(0.281)
0.147
(0.315)
0.221
(0.409)
3q loss 33 (18%) 151 0.905
(0.951)
0.912
(0.954)
0.106
(0.261)
0.661
(0.808)
0.779
(0.884)
0.597
(0.765)
0.765
(0.878)
0.912
(0.954)
0.912
(0.954)
0.899
(0.947)
6p loss 38 (21%) 146 0.0839
(0.227)
0.286
(0.479)
0.571
(0.753)
0.915
(0.956)
0.0832
(0.226)
0.566
(0.749)
0.224
(0.413)
0.288
(0.48)
0.584
(0.76)
0.386
(0.592)
6q loss 40 (22%) 144 0.129
(0.291)
0.282
(0.474)
0.436
(0.641)
0.604
(0.768)
0.252
(0.444)
0.812
(0.9)
0.258
(0.448)
0.616
(0.776)
0.678
(0.814)
0.425
(0.632)
7p loss 13 (7%) 171 1
(1.00)
0.827
(0.909)
0.846
(0.92)
0.116
(0.277)
0.0565
(0.176)
0.64
(0.797)
0.47
(0.666)
0.581
(0.76)
0.54
(0.731)
0.383
(0.591)
8q loss 21 (11%) 163 0.12
(0.279)
0.748
(0.865)
0.898
(0.947)
0.946
(0.971)
0.132
(0.296)
0.117
(0.277)
0.674
(0.814)
0.563
(0.748)
0.675
(0.814)
0.947
(0.971)
11p loss 52 (28%) 132 0.139
(0.305)
0.599
(0.765)
0.94
(0.968)
0.73
(0.852)
0.447
(0.648)
0.919
(0.957)
0.799
(0.897)
0.649
(0.804)
0.939
(0.968)
0.784
(0.884)
17q loss 26 (14%) 158 0.299
(0.493)
0.873
(0.929)
0.993
(1.00)
0.671
(0.814)
0.241
(0.433)
0.512
(0.71)
0.857
(0.923)
0.943
(0.97)
0.652
(0.806)
0.957
(0.978)
20p loss 19 (10%) 165 1
(1.00)
0.975
(0.99)
0.495
(0.693)
0.822
(0.906)
0.623
(0.778)
0.152
(0.318)
0.861
(0.923)
0.418
(0.627)
0.898
(0.947)
0.475
(0.67)
20q loss 6 (3%) 178 0.561
(0.747)
0.314
(0.509)
0.282
(0.474)
0.765
(0.878)
0.471
(0.667)
1
(1.00)
0.679
(0.814)
0.636
(0.792)
0.375
(0.581)
0.858
(0.923)
'1q gain' versus 'CN_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.061

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
1Q GAIN MUTATED 25 5 34
1Q GAIN WILD-TYPE 49 28 43

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
2P GAIN MUTATED 23 4 34
2P GAIN WILD-TYPE 51 29 43

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0078

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
2P GAIN MUTATED 13 10 2 23 9 1 3
2P GAIN WILD-TYPE 23 32 0 18 28 16 6

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
2P GAIN MUTATED 20 5 13 14 0 9
2P GAIN WILD-TYPE 53 9 29 15 9 7

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.1

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
2P GAIN MUTATED 19 31 7 2
2P GAIN WILD-TYPE 45 36 28 10

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 0.00955 (Fisher's exact test), Q value = 0.054

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
2Q GAIN MUTATED 21 2 24
2Q GAIN WILD-TYPE 53 31 53

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
2Q GAIN MUTATED 12 9 1 16 5 1 3
2Q GAIN WILD-TYPE 24 33 1 25 32 16 6

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

'3p gain' versus 'CN_CNMF'

P value = 0.00491 (Fisher's exact test), Q value = 0.033

Table S8.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
3P GAIN MUTATED 16 0 15
3P GAIN WILD-TYPE 58 33 62

Figure S8.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S9.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
3Q GAIN MUTATED 31 0 46
3Q GAIN WILD-TYPE 43 33 31

Figure S9.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00528 (Fisher's exact test), Q value = 0.034

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
3Q GAIN MUTATED 13 18 0 24 18 1 3
3Q GAIN WILD-TYPE 23 24 2 17 19 16 6

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'RPPA_CNMF'

P value = 0.00355 (Fisher's exact test), Q value = 0.028

Table S11.  Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
4Q GAIN MUTATED 1 6 7 0 0
4Q GAIN WILD-TYPE 25 22 23 34 8

Figure S11.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0047 (Fisher's exact test), Q value = 0.032

Table S12.  Gene #8: '4q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
4Q GAIN MUTATED 1 6 4 3 0
4Q GAIN WILD-TYPE 22 15 18 23 34

Figure S12.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0057

Table S13.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
5P GAIN MUTATED 26 6 43
5P GAIN WILD-TYPE 48 27 34

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.028

Table S14.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
5P GAIN MUTATED 11 12 0 25 19 3 5
5P GAIN WILD-TYPE 25 30 2 16 18 14 4

Figure S14.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.13

Table S15.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
5P GAIN MUTATED 23 4 19 18 2 9
5P GAIN WILD-TYPE 50 10 23 11 7 7

Figure S15.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.082

Table S16.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
5P GAIN MUTATED 23 4 48
5P GAIN WILD-TYPE 44 16 48

Figure S16.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0399 (Fisher's exact test), Q value = 0.14

Table S17.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
5P GAIN MUTATED 18 9 33 15
5P GAIN WILD-TYPE 44 17 29 18

Figure S17.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00771 (Fisher's exact test), Q value = 0.045

Table S18.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
5P GAIN MUTATED 14 13 48
5P GAIN WILD-TYPE 41 16 46

Figure S18.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.12

Table S19.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
6P GAIN MUTATED 22 1 4 4 3 5
6P GAIN WILD-TYPE 48 14 6 14 25 37

Figure S19.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.1

Table S20.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
6P GAIN MUTATED 21 3 8 7
6P GAIN WILD-TYPE 41 23 54 26

Figure S20.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.088

Table S21.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
6P GAIN MUTATED 22 10 4 3
6P GAIN WILD-TYPE 42 57 31 9

Figure S21.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.059

Table S22.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
6P GAIN MUTATED 20 4 15
6P GAIN WILD-TYPE 35 25 79

Figure S22.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.13

Table S23.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
7Q GAIN MUTATED 37 9 41
7Q GAIN WILD-TYPE 37 24 36

Figure S23.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.14

Table S24.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
9P GAIN MUTATED 4 5 0 2 1 4
9P GAIN WILD-TYPE 66 10 10 16 27 38

Figure S24.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.093

Table S25.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
9Q GAIN MUTATED 6 7 17 3
9Q GAIN WILD-TYPE 56 19 45 30

Figure S25.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 0.036

Table S26.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
10P GAIN MUTATED 25 5 10
10P GAIN WILD-TYPE 49 28 67

Figure S26.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.14

Table S27.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
10P GAIN MUTATED 22 2 3 3 1 9
10P GAIN WILD-TYPE 48 13 7 15 27 33

Figure S27.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.028

Table S28.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
10Q GAIN MUTATED 21 3 7
10Q GAIN WILD-TYPE 53 30 70

Figure S28.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.072

Table S29.  Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
10Q GAIN MUTATED 12 8 1 3 6 0 1
10Q GAIN WILD-TYPE 24 34 1 38 31 17 8

Figure S29.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.12

Table S30.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
10Q GAIN MUTATED 15 5 10
10Q GAIN WILD-TYPE 40 24 84

Figure S30.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.15

Table S31.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
11P GAIN MUTATED 17 2 20
11P GAIN WILD-TYPE 57 31 57

Figure S31.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0057

Table S32.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
12P GAIN MUTATED 16 5 36
12P GAIN WILD-TYPE 58 28 41

Figure S32.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.021

Table S33.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
12P GAIN MUTATED 7 9 0 23 9 4 5
12P GAIN WILD-TYPE 29 33 2 18 28 13 4

Figure S33.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00341 (Fisher's exact test), Q value = 0.027

Table S34.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
12P GAIN MUTATED 13 7 12 15 2 8
12P GAIN WILD-TYPE 60 7 30 14 7 8

Figure S34.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00541 (Fisher's exact test), Q value = 0.035

Table S35.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
12P GAIN MUTATED 14 3 40
12P GAIN WILD-TYPE 53 17 56

Figure S35.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0025 (Fisher's exact test), Q value = 0.022

Table S36.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
12P GAIN MUTATED 12 5 30 9
12P GAIN WILD-TYPE 50 21 32 24

Figure S36.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00876 (Fisher's exact test), Q value = 0.05

Table S37.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
12P GAIN MUTATED 14 31 8 2
12P GAIN WILD-TYPE 50 36 27 10

Figure S37.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.066

Table S38.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
12P GAIN MUTATED 10 7 38
12P GAIN WILD-TYPE 45 22 56

Figure S38.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.12

Table S39.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
12Q GAIN MUTATED 14 2 21
12Q GAIN WILD-TYPE 60 31 56

Figure S39.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.002

Table S40.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
13Q GAIN MUTATED 30 5 9
13Q GAIN WILD-TYPE 44 28 68

Figure S40.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.012

Table S41.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
13Q GAIN MUTATED 14 17 0 7 2 2 2
13Q GAIN WILD-TYPE 22 25 2 34 35 15 7

Figure S41.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0019

Table S42.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
13Q GAIN MUTATED 31 0 4 5 2 2
13Q GAIN WILD-TYPE 42 14 38 24 7 14

Figure S42.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S43.  Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
13Q GAIN MUTATED 24 11 9
13Q GAIN WILD-TYPE 43 9 87

Figure S43.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S44.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
13Q GAIN MUTATED 31 4 1 3 2 3
13Q GAIN WILD-TYPE 39 11 9 15 26 39

Figure S44.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0012

Table S45.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
13Q GAIN MUTATED 25 10 5 4
13Q GAIN WILD-TYPE 37 16 57 29

Figure S45.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0012

Table S46.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
13Q GAIN MUTATED 28 8 4 4
13Q GAIN WILD-TYPE 36 59 31 8

Figure S46.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S47.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
13Q GAIN MUTATED 23 12 9
13Q GAIN WILD-TYPE 32 17 85

Figure S47.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.11

Table S48.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
14Q GAIN MUTATED 12 10 27
14Q GAIN WILD-TYPE 62 23 50

Figure S48.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.074

Table S49.  Gene #26: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
14Q GAIN MUTATED 4 5 9 17 4
14Q GAIN WILD-TYPE 22 23 21 17 4

Figure S49.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.078

Table S50.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
14Q GAIN MUTATED 13 2 34
14Q GAIN WILD-TYPE 54 18 62

Figure S50.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.13

Table S51.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
14Q GAIN MUTATED 11 4 24 9
14Q GAIN WILD-TYPE 51 22 38 24

Figure S51.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.08

Table S52.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
14Q GAIN MUTATED 11 22 8 7
14Q GAIN WILD-TYPE 53 45 27 5

Figure S52.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.14

Table S53.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
14Q GAIN MUTATED 10 5 33
14Q GAIN WILD-TYPE 45 24 61

Figure S53.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.07

Table S54.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
16P GAIN MUTATED 11 4 25
16P GAIN WILD-TYPE 63 29 52

Figure S54.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.13

Table S55.  Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
16P GAIN MUTATED 7 4 1 14 11 3 0
16P GAIN WILD-TYPE 29 38 1 27 26 14 9

Figure S55.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00502 (Fisher's exact test), Q value = 0.033

Table S56.  Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16P GAIN MUTATED 12 0 28
16P GAIN WILD-TYPE 55 20 68

Figure S56.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.13

Table S57.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16P GAIN MUTATED 8 4 21 7
16P GAIN WILD-TYPE 54 22 41 26

Figure S57.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.16

Table S58.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
16P GAIN MUTATED 7 20 8 3
16P GAIN WILD-TYPE 57 47 27 9

Figure S58.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.00422 (Fisher's exact test), Q value = 0.03

Table S59.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
16Q GAIN MUTATED 9 4 25
16Q GAIN WILD-TYPE 65 29 52

Figure S59.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.16

Table S60.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
16Q GAIN MUTATED 6 4 1 12 12 3 0
16Q GAIN WILD-TYPE 30 38 1 29 25 14 9

Figure S60.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.11

Table S61.  Gene #29: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
16Q GAIN MUTATED 0 3 7 7 8
16Q GAIN WILD-TYPE 23 18 15 19 26

Figure S61.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.15

Table S62.  Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16Q GAIN MUTATED 9 2 27
16Q GAIN WILD-TYPE 58 18 69

Figure S62.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.12

Table S63.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16Q GAIN MUTATED 6 5 19 8
16Q GAIN WILD-TYPE 56 21 43 25

Figure S63.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.1

Table S64.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
16Q GAIN MUTATED 6 19 7 4
16Q GAIN WILD-TYPE 58 48 28 8

Figure S64.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.079

Table S65.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
17P GAIN MUTATED 12 1 19
17P GAIN WILD-TYPE 62 32 58

Figure S65.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.11

Table S66.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
18P GAIN MUTATED 14 6 7 4 9 9
18P GAIN WILD-TYPE 56 9 3 14 19 33

Figure S66.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.061

Table S67.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
18Q GAIN MUTATED 7 3 5 2 5 2
18Q GAIN WILD-TYPE 63 12 5 16 23 40

Figure S67.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0083

Table S68.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
20P GAIN MUTATED 52 10 45
20P GAIN WILD-TYPE 22 23 32

Figure S68.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S69.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
20Q GAIN MUTATED 60 12 42
20Q GAIN WILD-TYPE 14 21 35

Figure S69.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.018

Table S70.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
20Q GAIN MUTATED 30 30 0 22 16 9 7
20Q GAIN WILD-TYPE 6 12 2 19 21 8 2

Figure S70.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.022

Table S71.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
20Q GAIN MUTATED 56 11 19 15 3 10
20Q GAIN WILD-TYPE 17 3 23 14 6 6

Figure S71.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00399 (Fisher's exact test), Q value = 0.029

Table S72.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
20Q GAIN MUTATED 51 14 49
20Q GAIN WILD-TYPE 16 6 47

Figure S72.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.012

Table S73.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
20Q GAIN MUTATED 52 11 9 10 15 16
20Q GAIN WILD-TYPE 18 4 1 8 13 26

Figure S73.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.022

Table S74.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
20Q GAIN MUTATED 48 18 33 14
20Q GAIN WILD-TYPE 14 8 29 19

Figure S74.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.1

Table S75.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
20Q GAIN MUTATED 48 33 23 8
20Q GAIN WILD-TYPE 16 34 12 4

Figure S75.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0032

Table S76.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
20Q GAIN MUTATED 45 21 46
20Q GAIN WILD-TYPE 10 8 48

Figure S76.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S77.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
22Q GAIN MUTATED 2 2 27
22Q GAIN WILD-TYPE 72 31 50

Figure S77.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S78.  Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
22Q GAIN MUTATED 1 2 0 17 9 1 1
22Q GAIN WILD-TYPE 35 40 2 24 28 16 8

Figure S78.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.03

Table S79.  Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
22Q GAIN MUTATED 1 3 6 14 1
22Q GAIN WILD-TYPE 25 25 24 20 7

Figure S79.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0069

Table S80.  Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
22Q GAIN MUTATED 1 0 3 9 12
22Q GAIN WILD-TYPE 22 21 19 17 22

Figure S80.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S81.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
22Q GAIN MUTATED 1 2 12 11 2 3
22Q GAIN WILD-TYPE 72 12 30 18 7 13

Figure S81.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S82.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
22Q GAIN MUTATED 3 0 28
22Q GAIN WILD-TYPE 64 20 68

Figure S82.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0032

Table S83.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
22Q GAIN MUTATED 3 3 1 6 3 15
22Q GAIN WILD-TYPE 67 12 9 12 25 27

Figure S83.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S84.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
22Q GAIN MUTATED 2 1 22 6
22Q GAIN WILD-TYPE 60 25 40 27

Figure S84.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S85.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
22Q GAIN MUTATED 2 25 3 1
22Q GAIN WILD-TYPE 62 42 32 11

Figure S85.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S86.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
22Q GAIN MUTATED 2 1 28
22Q GAIN WILD-TYPE 53 28 66

Figure S86.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.13

Table S87.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
XQ GAIN MUTATED 1 10 6 10 2
XQ GAIN WILD-TYPE 25 18 24 24 6

Figure S87.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.11

Table S88.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
XQ GAIN MUTATED 11 3 14 11 0 2
XQ GAIN WILD-TYPE 62 11 28 18 9 14

Figure S88.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.11

Table S89.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
XQ GAIN MUTATED 8 5 28
XQ GAIN WILD-TYPE 59 15 68

Figure S89.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.12

Table S90.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
XQ GAIN MUTATED 12 1 19 8
XQ GAIN WILD-TYPE 50 25 43 25

Figure S90.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.16

Table S91.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
XQ GAIN MUTATED 12 21 3 3
XQ GAIN WILD-TYPE 52 46 32 9

Figure S91.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0096

Table S92.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
1P LOSS MUTATED 24 1 13
1P LOSS WILD-TYPE 50 32 64

Figure S92.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S93.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
1P LOSS MUTATED 8 16 0 13 0 0 1
1P LOSS WILD-TYPE 28 26 2 28 37 17 8

Figure S93.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0099

Table S94.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
1P LOSS MUTATED 23 1 2 10 0 2
1P LOSS WILD-TYPE 50 13 40 19 9 14

Figure S94.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.13

Table S95.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
1P LOSS MUTATED 20 5 13
1P LOSS WILD-TYPE 47 15 83

Figure S95.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.12

Table S96.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
1P LOSS MUTATED 19 6 11 2
1P LOSS WILD-TYPE 43 20 51 31

Figure S96.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.081

Table S97.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
1P LOSS MUTATED 21 11 5 0
1P LOSS WILD-TYPE 43 56 30 12

Figure S97.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.11

Table S98.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
1P LOSS MUTATED 18 6 13
1P LOSS WILD-TYPE 37 23 81

Figure S98.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.16

Table S99.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
1Q LOSS MUTATED 14 1 7
1Q LOSS WILD-TYPE 60 32 70

Figure S99.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.12

Table S100.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
1Q LOSS MUTATED 12 5 1 1 1 2
1Q LOSS WILD-TYPE 58 10 9 17 27 40

Figure S100.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.058

Table S101.  Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
2P LOSS MUTATED 1 3 3 0 1 2
2P LOSS WILD-TYPE 72 11 39 29 8 14

Figure S101.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.0091

Table S102.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
2P LOSS MUTATED 2 0 1 7
2P LOSS WILD-TYPE 60 26 61 26

Figure S102.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.069

Table S103.  Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
2Q LOSS MUTATED 3 5 4 2 1 3
2Q LOSS WILD-TYPE 70 9 38 27 8 13

Figure S103.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 0.12

Table S104.  Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
2Q LOSS MUTATED 2 2 14
2Q LOSS WILD-TYPE 65 18 82

Figure S104.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0072 (Fisher's exact test), Q value = 0.043

Table S105.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
2Q LOSS MUTATED 3 1 5 9
2Q LOSS WILD-TYPE 59 25 57 24

Figure S105.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S106.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
3P LOSS MUTATED 27 11 54
3P LOSS WILD-TYPE 47 22 23

Figure S106.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0026

Table S107.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
3P LOSS MUTATED 11 14 0 30 25 7 5
3P LOSS WILD-TYPE 25 28 2 11 12 10 4

Figure S107.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

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

Table S108.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
3P LOSS MUTATED 25 8 27 22 4 5
3P LOSS WILD-TYPE 48 6 15 7 5 11

Figure S108.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S109.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
3P LOSS MUTATED 17 9 65
3P LOSS WILD-TYPE 50 11 31

Figure S109.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.013

Table S110.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
3P LOSS MUTATED 25 6 3 11 16 31
3P LOSS WILD-TYPE 45 9 7 7 12 11

Figure S110.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S111.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
3P LOSS MUTATED 20 7 42 23
3P LOSS WILD-TYPE 42 19 20 10

Figure S111.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.011

Table S112.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
3P LOSS MUTATED 21 45 17 7
3P LOSS WILD-TYPE 43 22 18 5

Figure S112.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S113.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
3P LOSS MUTATED 17 9 64
3P LOSS WILD-TYPE 38 20 30

Figure S113.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0094

Table S114.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
4P LOSS MUTATED 47 9 49
4P LOSS WILD-TYPE 27 24 28

Figure S114.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.03

Table S115.  Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
4P LOSS MUTATED 20 25 0 31 22 5 2
4P LOSS WILD-TYPE 16 17 2 10 15 12 7

Figure S115.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.12

Table S116.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
4P LOSS MUTATED 41 7 25 23 2 7
4P LOSS WILD-TYPE 32 7 17 6 7 9

Figure S116.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.09

Table S117.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
4P LOSS MUTATED 34 44 14 10
4P LOSS WILD-TYPE 30 23 21 2

Figure S117.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S118.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
4Q LOSS MUTATED 47 4 37
4Q LOSS WILD-TYPE 27 29 40

Figure S118.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00903 (Fisher's exact test), Q value = 0.051

Table S119.  Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
4Q LOSS MUTATED 20 24 0 23 17 3 1
4Q LOSS WILD-TYPE 16 18 2 18 20 14 8

Figure S119.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.032

Table S120.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
5P LOSS MUTATED 28 6 12
5P LOSS WILD-TYPE 46 27 65

Figure S120.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0093

Table S121.  Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
5P LOSS MUTATED 16 17 0 7 4 1 1
5P LOSS WILD-TYPE 20 25 2 34 33 16 8

Figure S121.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S122.  Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
5P LOSS MUTATED 28 8 3 5 1 1
5P LOSS WILD-TYPE 45 6 39 24 8 15

Figure S122.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0019

Table S123.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
5P LOSS MUTATED 22 11 13
5P LOSS WILD-TYPE 45 9 83

Figure S123.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S124.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
5P LOSS MUTATED 30 1 4 5 2 3
5P LOSS WILD-TYPE 40 14 6 13 26 39

Figure S124.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00082

Table S125.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
5P LOSS MUTATED 29 5 7 4
5P LOSS WILD-TYPE 33 21 55 29

Figure S125.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0017

Table S126.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
5P LOSS MUTATED 28 12 2 1
5P LOSS WILD-TYPE 36 55 33 11

Figure S126.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S127.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
5P LOSS MUTATED 27 5 11
5P LOSS WILD-TYPE 28 24 83

Figure S127.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.017

Table S128.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
5Q LOSS MUTATED 45 8 34
5Q LOSS WILD-TYPE 29 25 43

Figure S128.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0034

Table S129.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
5Q LOSS MUTATED 23 23 0 26 9 4 2
5Q LOSS WILD-TYPE 13 19 2 15 28 13 7

Figure S129.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.032

Table S130.  Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
5Q LOSS MUTATED 41 9 9 16 4 8
5Q LOSS WILD-TYPE 32 5 33 13 5 8

Figure S130.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.13

Table S131.  Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
7Q LOSS MUTATED 10 4 8 0 0 1
7Q LOSS WILD-TYPE 63 10 34 29 9 15

Figure S131.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.1

Table S132.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
8P LOSS MUTATED 25 5 32
8P LOSS WILD-TYPE 49 28 45

Figure S132.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.098

Table S133.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
9P LOSS MUTATED 46 11 43
9P LOSS WILD-TYPE 28 22 34

Figure S133.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.093

Table S134.  Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
9P LOSS MUTATED 43 12 24 10 4 6
9P LOSS WILD-TYPE 30 2 18 19 5 10

Figure S134.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.082

Table S135.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
9Q LOSS MUTATED 27 5 33
9Q LOSS WILD-TYPE 47 28 44

Figure S135.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.11

Table S136.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
9Q LOSS MUTATED 18 7 0 16 17 5 2
9Q LOSS WILD-TYPE 18 35 2 25 20 12 7

Figure S136.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.12

Table S137.  Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
9Q LOSS MUTATED 22 11 15 10 2 5
9Q LOSS WILD-TYPE 51 3 27 19 7 11

Figure S137.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.014

Table S138.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
10P LOSS MUTATED 15 4 32
10P LOSS WILD-TYPE 59 29 45

Figure S138.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00373 (Fisher's exact test), Q value = 0.028

Table S139.  Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
10P LOSS MUTATED 3 9 0 20 12 4 3
10P LOSS WILD-TYPE 33 33 2 21 25 13 6

Figure S139.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00725 (Fisher's exact test), Q value = 0.043

Table S140.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
10P LOSS MUTATED 12 2 15 15 2 5
10P LOSS WILD-TYPE 61 12 27 14 7 11

Figure S140.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00977 (Fisher's exact test), Q value = 0.055

Table S141.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
10P LOSS MUTATED 12 3 36
10P LOSS WILD-TYPE 55 17 60

Figure S141.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.1

Table S142.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
10P LOSS MUTATED 11 8 2 5 10 15
10P LOSS WILD-TYPE 59 7 8 13 18 27

Figure S142.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00572 (Fisher's exact test), Q value = 0.036

Table S143.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
10P LOSS MUTATED 8 7 24 12
10P LOSS WILD-TYPE 54 19 38 21

Figure S143.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.076

Table S144.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
10P LOSS MUTATED 10 27 10 4
10P LOSS WILD-TYPE 54 40 25 8

Figure S144.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.022

Table S145.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
10P LOSS MUTATED 7 8 36
10P LOSS WILD-TYPE 48 21 58

Figure S145.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0015

Table S146.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
10Q LOSS MUTATED 12 4 34
10Q LOSS WILD-TYPE 62 29 43

Figure S146.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0013

Table S147.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
10Q LOSS MUTATED 3 7 0 23 9 5 3
10Q LOSS WILD-TYPE 33 35 2 18 28 12 6

Figure S147.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.0053 (Fisher's exact test), Q value = 0.034

Table S148.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
10Q LOSS MUTATED 11 3 13 15 4 4
10Q LOSS WILD-TYPE 62 11 29 14 5 12

Figure S148.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.013

Table S149.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
10Q LOSS MUTATED 11 2 37
10Q LOSS WILD-TYPE 56 18 59

Figure S149.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.1

Table S150.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
10Q LOSS MUTATED 10 6 2 5 11 16
10Q LOSS WILD-TYPE 60 9 8 13 17 26

Figure S150.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.017

Table S151.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
10Q LOSS MUTATED 8 5 26 11
10Q LOSS WILD-TYPE 54 21 36 22

Figure S151.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00651 (Fisher's exact test), Q value = 0.04

Table S152.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
10Q LOSS MUTATED 9 27 10 4
10Q LOSS WILD-TYPE 55 40 25 8

Figure S152.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.011

Table S153.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
10Q LOSS MUTATED 7 6 37
10Q LOSS WILD-TYPE 48 23 57

Figure S153.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0069

Table S154.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
11Q LOSS MUTATED 18 5 37
11Q LOSS WILD-TYPE 56 28 40

Figure S154.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.1

Table S155.  Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
11Q LOSS MUTATED 11 8 0 17 18 2 4
11Q LOSS WILD-TYPE 25 34 2 24 19 15 5

Figure S155.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 0.036

Table S156.  Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
11Q LOSS MUTATED 16 10 14 11 1 7
11Q LOSS WILD-TYPE 57 4 28 18 8 9

Figure S156.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.11

Table S157.  Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
11Q LOSS MUTATED 14 6 39
11Q LOSS WILD-TYPE 53 14 57

Figure S157.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.1

Table S158.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
12P LOSS MUTATED 21 4 9
12P LOSS WILD-TYPE 53 29 68

Figure S158.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.12

Table S159.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
12P LOSS MUTATED 14 9 0 4 5 1 1
12P LOSS WILD-TYPE 22 33 2 37 32 16 8

Figure S159.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.12

Table S160.  Gene #64: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
12P LOSS MUTATED 10 3 5 4 3
12P LOSS WILD-TYPE 13 18 17 22 31

Figure S160.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.055

Table S161.  Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
12P LOSS MUTATED 22 4 3 4 0 1
12P LOSS WILD-TYPE 51 10 39 25 9 15

Figure S161.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.016

Table S162.  Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
12P LOSS MUTATED 18 7 9
12P LOSS WILD-TYPE 49 13 87

Figure S162.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.11

Table S163.  Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
12P LOSS MUTATED 21 2 3 2 3 3
12P LOSS WILD-TYPE 49 13 7 16 25 39

Figure S163.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.028

Table S164.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
12P LOSS MUTATED 15 10 5 4
12P LOSS WILD-TYPE 47 16 57 29

Figure S164.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.15

Table S165.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
12P LOSS MUTATED 19 7 6 2
12P LOSS WILD-TYPE 45 60 29 10

Figure S165.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.007

Table S166.  Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
12P LOSS MUTATED 13 12 9
12P LOSS WILD-TYPE 42 17 85

Figure S166.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.13

Table S167.  Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
12Q LOSS MUTATED 12 8 0 5 2 2 3
12Q LOSS WILD-TYPE 24 34 2 36 35 15 6

Figure S167.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.061

Table S168.  Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
12Q LOSS MUTATED 15 7 10
12Q LOSS WILD-TYPE 52 13 86

Figure S168.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.14

Table S169.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
12Q LOSS MUTATED 14 8 8 2
12Q LOSS WILD-TYPE 48 18 54 31

Figure S169.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.11

Table S170.  Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
12Q LOSS MUTATED 19 7 5 1
12Q LOSS WILD-TYPE 45 60 30 11

Figure S170.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.057

Table S171.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
12Q LOSS MUTATED 12 10 10
12Q LOSS WILD-TYPE 43 19 84

Figure S171.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.026

Table S172.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
13Q LOSS MUTATED 25 5 37
13Q LOSS WILD-TYPE 49 28 40

Figure S172.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.13

Table S173.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
13Q LOSS MUTATED 22 3 42
13Q LOSS WILD-TYPE 45 17 54

Figure S173.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.13

Table S174.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
13Q LOSS MUTATED 16 33 12 4
13Q LOSS WILD-TYPE 48 34 23 8

Figure S174.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S175.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
14Q LOSS MUTATED 33 0 12
14Q LOSS WILD-TYPE 41 33 65

Figure S175.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.092

Table S176.  Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
14Q LOSS MUTATED 14 15 0 6 6 1 3
14Q LOSS WILD-TYPE 22 27 2 35 31 16 6

Figure S176.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.03

Table S177.  Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
14Q LOSS MUTATED 10 12 7 3 0
14Q LOSS WILD-TYPE 16 16 23 31 8

Figure S177.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00289 (Fisher's exact test), Q value = 0.024

Table S178.  Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
14Q LOSS MUTATED 7 11 6 6 2
14Q LOSS WILD-TYPE 16 10 16 20 32

Figure S178.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 0.031

Table S179.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
14Q LOSS MUTATED 27 6 6 4 0 2
14Q LOSS WILD-TYPE 46 8 36 25 9 14

Figure S179.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.088

Table S180.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
14Q LOSS MUTATED 24 5 16
14Q LOSS WILD-TYPE 43 15 80

Figure S180.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.082

Table S181.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
14Q LOSS MUTATED 26 2 4 4 4 5
14Q LOSS WILD-TYPE 44 13 6 14 24 37

Figure S181.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S182.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
14Q LOSS MUTATED 26 4 10 5
14Q LOSS WILD-TYPE 36 22 52 28

Figure S182.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.14

Table S183.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
14Q LOSS MUTATED 24 11 8 2
14Q LOSS WILD-TYPE 40 56 27 10

Figure S183.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.022

Table S184.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
14Q LOSS MUTATED 23 7 15
14Q LOSS WILD-TYPE 32 22 79

Figure S184.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.13

Table S185.  Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
15Q LOSS MUTATED 28 6 22
15Q LOSS WILD-TYPE 39 14 74

Figure S185.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00432 (Fisher's exact test), Q value = 0.03

Table S186.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
15Q LOSS MUTATED 18 16 14 8
15Q LOSS WILD-TYPE 44 10 48 25

Figure S186.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0069

Table S187.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
15Q LOSS MUTATED 16 18 22
15Q LOSS WILD-TYPE 39 11 72

Figure S187.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0087

Table S188.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
16P LOSS MUTATED 33 8 13
16P LOSS WILD-TYPE 41 25 64

Figure S188.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00728 (Fisher's exact test), Q value = 0.043

Table S189.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
16P LOSS MUTATED 16 19 0 6 7 5 1
16P LOSS WILD-TYPE 20 23 2 35 30 12 8

Figure S189.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.026

Table S190.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
16P LOSS MUTATED 31 6 4 6 2 5
16P LOSS WILD-TYPE 42 8 38 23 7 11

Figure S190.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0019

Table S191.  Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16P LOSS MUTATED 27 11 16
16P LOSS WILD-TYPE 40 9 80

Figure S191.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00675 (Fisher's exact test), Q value = 0.041

Table S192.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
16P LOSS MUTATED 30 6 2 5 5 5
16P LOSS WILD-TYPE 40 9 8 13 23 37

Figure S192.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0036

Table S193.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16P LOSS MUTATED 30 8 10 5
16P LOSS WILD-TYPE 32 18 52 28

Figure S193.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0057

Table S194.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
16P LOSS MUTATED 30 10 7 4
16P LOSS WILD-TYPE 34 57 28 8

Figure S194.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0038

Table S195.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
16P LOSS MUTATED 25 11 15
16P LOSS WILD-TYPE 30 18 79

Figure S195.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0012

Table S196.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
16Q LOSS MUTATED 35 8 10
16Q LOSS WILD-TYPE 39 25 67

Figure S196.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0063

Table S197.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
16Q LOSS MUTATED 18 18 0 6 4 4 3
16Q LOSS WILD-TYPE 18 24 2 35 33 13 6

Figure S197.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.13

Table S198.  Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
16Q LOSS MUTATED 10 10 4 4 2
16Q LOSS WILD-TYPE 16 18 26 30 6

Figure S198.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.12

Table S199.  Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
16Q LOSS MUTATED 9 9 3 3 6
16Q LOSS WILD-TYPE 14 12 19 23 28

Figure S199.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0062

Table S200.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
16Q LOSS MUTATED 32 6 5 3 1 6
16Q LOSS WILD-TYPE 41 8 37 26 8 10

Figure S200.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S201.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16Q LOSS MUTATED 31 9 13
16Q LOSS WILD-TYPE 36 11 83

Figure S201.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0026

Table S202.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
16Q LOSS MUTATED 33 4 2 5 2 6
16Q LOSS WILD-TYPE 37 11 8 13 26 36

Figure S202.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S203.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16Q LOSS MUTATED 31 9 8 4
16Q LOSS WILD-TYPE 31 17 54 29

Figure S203.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S204.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
16Q LOSS MUTATED 33 10 5 2
16Q LOSS WILD-TYPE 31 57 30 10

Figure S204.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S205.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
16Q LOSS MUTATED 26 12 12
16Q LOSS WILD-TYPE 29 17 82

Figure S205.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0021

Table S206.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
17P LOSS MUTATED 43 8 21
17P LOSS WILD-TYPE 31 25 56

Figure S206.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0083

Table S207.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
17P LOSS MUTATED 18 26 1 15 7 4 1
17P LOSS WILD-TYPE 18 16 1 26 30 13 8

Figure S207.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.078

Table S208.  Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
17P LOSS MUTATED 40 6 10 9 3 4
17P LOSS WILD-TYPE 33 8 32 20 6 12

Figure S208.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.014

Table S209.  Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
17P LOSS MUTATED 36 10 26
17P LOSS WILD-TYPE 31 10 70

Figure S209.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00455 (Fisher's exact test), Q value = 0.031

Table S210.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
17P LOSS MUTATED 39 6 5 6 6 10
17P LOSS WILD-TYPE 31 9 5 12 22 32

Figure S210.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.019

Table S211.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
17P LOSS MUTATED 33 14 18 7
17P LOSS WILD-TYPE 29 12 44 26

Figure S211.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.15

Table S212.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
17P LOSS MUTATED 34 22 11 3
17P LOSS WILD-TYPE 30 45 24 9

Figure S212.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0036

Table S213.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
17P LOSS MUTATED 29 17 24
17P LOSS WILD-TYPE 26 12 70

Figure S213.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S214.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
18P LOSS MUTATED 43 5 21
18P LOSS WILD-TYPE 31 28 56

Figure S214.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.086

Table S215.  Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
18P LOSS MUTATED 18 23 0 9 12 4 3
18P LOSS WILD-TYPE 18 19 2 32 25 13 6

Figure S215.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.082

Table S216.  Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
18P LOSS MUTATED 39 3 11 8 2 5
18P LOSS WILD-TYPE 34 11 31 21 7 11

Figure S216.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00395 (Fisher's exact test), Q value = 0.029

Table S217.  Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
18P LOSS MUTATED 33 10 25
18P LOSS WILD-TYPE 34 10 71

Figure S217.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00368 (Fisher's exact test), Q value = 0.028

Table S218.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
18P LOSS MUTATED 38 2 1 5 11 12
18P LOSS WILD-TYPE 32 13 9 13 17 30

Figure S218.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.092

Table S219.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
18P LOSS MUTATED 31 12 19 7
18P LOSS WILD-TYPE 31 14 43 26

Figure S219.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00878 (Fisher's exact test), Q value = 0.05

Table S220.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
18P LOSS MUTATED 31 15 15 6
18P LOSS WILD-TYPE 33 52 20 6

Figure S220.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00566 (Fisher's exact test), Q value = 0.036

Table S221.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
18P LOSS MUTATED 28 14 25
18P LOSS WILD-TYPE 27 15 69

Figure S221.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0012

Table S222.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
18Q LOSS MUTATED 54 9 40
18Q LOSS WILD-TYPE 20 24 37

Figure S222.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.12

Table S223.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
18Q LOSS MUTATED 24 29 0 16 21 7 6
18Q LOSS WILD-TYPE 12 13 2 25 16 10 3

Figure S223.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00528 (Fisher's exact test), Q value = 0.034

Table S224.  Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
18Q LOSS MUTATED 51 3 24 13 5 6
18Q LOSS WILD-TYPE 22 11 18 16 4 10

Figure S224.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.09

Table S225.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
18Q LOSS MUTATED 44 14 44
18Q LOSS WILD-TYPE 23 6 52

Figure S225.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.022

Table S226.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
18Q LOSS MUTATED 49 8 1 6 15 24
18Q LOSS WILD-TYPE 21 7 9 12 13 18

Figure S226.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.004

Table S227.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
18Q LOSS MUTATED 35 23 34 11
18Q LOSS WILD-TYPE 27 3 28 22

Figure S227.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.15

Table S228.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
18Q LOSS MUTATED 42 29 23 7
18Q LOSS WILD-TYPE 22 38 12 5

Figure S228.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0026

Table S229.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
18Q LOSS MUTATED 31 26 44
18Q LOSS WILD-TYPE 24 3 50

Figure S229.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.15

Table S230.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
19P LOSS MUTATED 26 6 32
19P LOSS WILD-TYPE 29 23 62

Figure S230.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.14

Table S231.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
19Q LOSS MUTATED 21 4 27
19Q LOSS WILD-TYPE 53 29 50

Figure S231.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.11

Table S232.  Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
19Q LOSS MUTATED 19 1 32
19Q LOSS WILD-TYPE 48 19 64

Figure S232.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.007 (Fisher's exact test), Q value = 0.043

Table S233.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
21Q LOSS MUTATED 51 12 45
21Q LOSS WILD-TYPE 23 21 32

Figure S233.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00855 (Fisher's exact test), Q value = 0.05

Table S234.  Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
21Q LOSS MUTATED 22 32 0 24 22 6 2
21Q LOSS WILD-TYPE 14 10 2 17 15 11 7

Figure S234.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S235.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
22Q LOSS MUTATED 46 8 19
22Q LOSS WILD-TYPE 28 25 58

Figure S235.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0097

Table S236.  Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 36 42 2 41 37 17 9
22Q LOSS MUTATED 23 23 0 10 10 5 2
22Q LOSS WILD-TYPE 13 19 2 31 27 12 7

Figure S236.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.069

Table S237.  Gene #80: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
22Q LOSS MUTATED 16 10 11 7 1
22Q LOSS WILD-TYPE 10 18 19 27 7

Figure S237.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0021

Table S238.  Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
22Q LOSS MUTATED 43 8 10 7 2 3
22Q LOSS WILD-TYPE 30 6 32 22 7 13

Figure S238.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0013

Table S239.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
22Q LOSS MUTATED 39 9 25
22Q LOSS WILD-TYPE 28 11 71

Figure S239.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00709 (Fisher's exact test), Q value = 0.043

Table S240.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 70 15 10 18 28 42
22Q LOSS MUTATED 39 5 5 7 8 9
22Q LOSS WILD-TYPE 31 10 5 11 20 33

Figure S240.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0026

Table S241.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
22Q LOSS MUTATED 38 11 14 10
22Q LOSS WILD-TYPE 24 15 48 23

Figure S241.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S242.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 67 35 12
22Q LOSS MUTATED 42 18 8 4
22Q LOSS WILD-TYPE 22 49 27 8

Figure S242.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00059

Table S243.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
22Q LOSS MUTATED 34 15 23
22Q LOSS WILD-TYPE 21 14 71

Figure S243.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.15

Table S244.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
XP LOSS MUTATED 14 7 6 15 2
XP LOSS WILD-TYPE 12 21 24 19 6

Figure S244.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.11

Table S245.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
XP LOSS MUTATED 25 8 11 13 2 1
XP LOSS WILD-TYPE 48 6 31 16 7 15

Figure S245.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0019

Table S246.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
XQ LOSS MUTATED 14 3 1 8 1
XQ LOSS WILD-TYPE 12 25 29 26 7

Figure S246.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.11

Table S247.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
XQ LOSS MUTATED 11 3 2 5 6
XQ LOSS WILD-TYPE 12 18 20 21 28

Figure S247.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.058

Table S248.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 73 14 42 29 9 16
XQ LOSS MUTATED 21 6 3 7 1 1
XQ LOSS WILD-TYPE 52 8 39 22 8 15

Figure S248.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00295 (Fisher's exact test), Q value = 0.024

Table S249.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
XQ LOSS MUTATED 22 3 6 8
XQ LOSS WILD-TYPE 40 23 56 25

Figure S249.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.07

Table S250.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 29 94
XQ LOSS MUTATED 19 4 14
XQ LOSS WILD-TYPE 36 25 80

Figure S250.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/22519067/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/22541001/ESCA-TP.transferedmergedcluster.txt

  • Number of patients = 184

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)