Correlation between copy number variations of arm-level result and molecular subtypes
Stomach Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C16Q1W1R
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16Q1W1R
Overview
Introduction

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

Summary

Testing the association between copy number variation 79 arm-level events and 10 molecular subtypes across 369 patients, 184 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

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

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

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

  • 6p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

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

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF'.

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

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 1p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 2p loss cnv correlated to 'CN_CNMF'.

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

  • 3p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 5p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 7p loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 7q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

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

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

  • 13q loss cnv correlated to 'CN_CNMF'.

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

  • 15q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', 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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', 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'.

  • 17q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

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

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

  • 20p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 184 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
5q loss 81 (22%) 288 1e-05
(0.0079) 		1e-05
(0.0079) 		0.62
(1.00) 		0.977
(1.00) 		1e-05
(0.0079) 		3e-05
(0.0204) 		2e-05
(0.0138) 		1e-05
(0.0079) 		2e-05
(0.0138) 		1e-05
(0.0079)
16p loss 77 (21%) 292 1e-05
(0.0079) 		0.00036
(0.22) 		0.811
(1.00) 		0.842
(1.00) 		1e-05
(0.0079) 		1e-05
(0.0079) 		2e-05
(0.0138) 		9e-05
(0.0591) 		2e-05
(0.0138) 		1e-05
(0.0079)
17p loss 131 (36%) 238 1e-05
(0.0079) 		1e-05
(0.0079) 		0.504
(1.00) 		0.0286
(1.00) 		1e-05
(0.0079) 		1e-05
(0.0079) 		0.00018
(0.115) 		4e-05
(0.0268) 		7e-05
(0.0463) 		1e-05
(0.0079)
19p loss 93 (25%) 276 1e-05
(0.0079) 		1e-05
(0.0079) 		0.00397
(1.00) 		0.0702
(1.00) 		1e-05
(0.0079) 		1e-05
(0.0079) 		1e-05
(0.0079) 		1e-05
(0.0079) 		1e-05
(0.0079) 		1e-05
(0.0079)
19q loss 72 (20%) 297 1e-05
(0.0079) 		1e-05
(0.0079) 		0.018
(1.00) 		0.144
(1.00) 		1e-05
(0.0079) 		3e-05
(0.0204) 		1e-05
(0.0079) 		1e-05
(0.0079) 		1e-05
(0.0079) 		1e-05
(0.0079)
20q gain 231 (63%) 138 1e-05
(0.0079) 		1e-05
(0.0079) 		0.0525
(1.00) 		0.227
(1.00) 		1e-05
(0.0079) 		1e-05
(0.0079) 		0.00019
(0.12) 		1e-05
(0.0079) 		0.0147
(1.00) 		1e-05
(0.0079)
9p loss 116 (31%) 253 1e-05
(0.0079) 		1e-05
(0.0079) 		0.00165
(0.912) 		0.00028
(0.174) 		1e-05
(0.0079) 		0.00013
(0.0841) 		0.00091
(0.536) 		3e-05
(0.0204) 		0.068
(1.00) 		0.0001
(0.0654)
16q loss 86 (23%) 283 1e-05
(0.0079) 		1e-05
(0.0079) 		0.0468
(1.00) 		0.0832
(1.00) 		1e-05
(0.0079) 		2e-05
(0.0138) 		0.00028
(0.174) 		0.00024
(0.15) 		0.00445
(1.00) 		3e-05
(0.0204)
6p gain 69 (19%) 300 1e-05
(0.0079) 		1e-05
(0.0079) 		0.0829
(1.00) 		0.298
(1.00) 		0.00024
(0.15) 		0.00405
(1.00) 		7e-05
(0.0463) 		0.00054
(0.325) 		0.00013
(0.0841) 		1e-05
(0.0079)
12p loss 48 (13%) 321 1e-05
(0.0079) 		1e-05
(0.0079) 		0.264
(1.00) 		0.0975
(1.00) 		9e-05
(0.0591) 		1e-05
(0.0079) 		0.0618
(1.00) 		1e-05
(0.0079) 		0.0244
(1.00) 		1e-05
(0.0079)
22q loss 116 (31%) 253 1e-05
(0.0079) 		1e-05
(0.0079) 		0.015
(1.00) 		0.00714
(1.00) 		0.00125
(0.715) 		0.00432
(1.00) 		4e-05
(0.0268) 		1e-05
(0.0079) 		0.0004
(0.243) 		1e-05
(0.0079)
5p gain 84 (23%) 285 1e-05
(0.0079) 		1e-05
(0.0079) 		0.263
(1.00) 		0.96
(1.00) 		1e-05
(0.0079) 		0.00469
(1.00) 		0.00193
(1.00) 		7e-05
(0.0463) 		0.00156
(0.872) 		1e-05
(0.0079)
6q gain 55 (15%) 314 1e-05
(0.0079) 		1e-05
(0.0079) 		0.119
(1.00) 		0.247
(1.00) 		0.00027
(0.168) 		0.0081
(1.00) 		0.00015
(0.0966) 		0.0335
(1.00) 		0.00011
(0.0717) 		0.00099
(0.574)
13q gain 129 (35%) 240 1e-05
(0.0079) 		0.00019
(0.12) 		0.57
(1.00) 		0.637
(1.00) 		0.0223
(1.00) 		6e-05
(0.04) 		0.00954
(1.00) 		0.00343
(1.00) 		0.00018
(0.115) 		7e-05
(0.0463)
4p loss 139 (38%) 230 1e-05
(0.0079) 		2e-05
(0.0138) 		0.28
(1.00) 		0.102
(1.00) 		0.00058
(0.348) 		0.00021
(0.133) 		0.00426
(1.00) 		1e-05
(0.0079) 		0.00161
(0.895) 		1e-05
(0.0079)
15q loss 78 (21%) 291 1e-05
(0.0079) 		0.00138
(0.781) 		0.0103
(1.00) 		0.648
(1.00) 		0.00015
(0.0966) 		0.00165
(0.912) 		0.00394
(1.00) 		0.00031
(0.192) 		0.00031
(0.192) 		0.00011
(0.0717)
18p gain 66 (18%) 303 1e-05
(0.0079) 		1e-05
(0.0079) 		0.0953
(1.00) 		0.0455
(1.00) 		0.0156
(1.00) 		0.00272
(1.00) 		0.00026
(0.162) 		0.00023
(0.145) 		0.00075
(0.445) 		0.00077
(0.457)
20p gain 201 (54%) 168 1e-05
(0.0079) 		0.00012
(0.0778) 		0.0849
(1.00) 		0.149
(1.00) 		0.0007
(0.418) 		1e-05
(0.0079) 		0.00614
(1.00) 		0.00054
(0.325) 		0.0279
(1.00) 		0.00011
(0.0717)
3q loss 47 (13%) 322 1e-05
(0.0079) 		0.00244
(1.00) 		0.208
(1.00) 		0.272
(1.00) 		0.0001
(0.0654) 		2e-05
(0.0138) 		0.00261
(1.00) 		0.00195
(1.00) 		0.00032
(0.197) 		0.00176
(0.968)
4q loss 137 (37%) 232 1e-05
(0.0079) 		3e-05
(0.0204) 		0.0707
(1.00) 		0.0222
(1.00) 		0.00622
(1.00) 		0.00107
(0.618) 		0.00789
(1.00) 		1e-05
(0.0079) 		0.00314
(1.00) 		1e-05
(0.0079)
17q loss 61 (17%) 308 1e-05
(0.0079) 		1e-05
(0.0079) 		0.398
(1.00) 		0.00977
(1.00) 		0.00105
(0.608) 		0.00338
(1.00) 		0.0424
(1.00) 		0.00034
(0.208) 		0.00531
(1.00) 		2e-05
(0.0138)
1q gain 88 (24%) 281 1e-05
(0.0079) 		0.00023
(0.145) 		0.0398
(1.00) 		0.177
(1.00) 		5e-05
(0.0333) 		0.00755
(1.00) 		0.0147
(1.00) 		0.00976
(1.00) 		0.00085
(0.502) 		0.0166
(1.00)
10p gain 85 (23%) 284 1e-05
(0.0079) 		2e-05
(0.0138) 		0.109
(1.00) 		0.43
(1.00) 		0.00164
(0.909) 		0.148
(1.00) 		0.199
(1.00) 		0.00047
(0.284) 		0.068
(1.00) 		0.00028
(0.174)
21q gain 21 (6%) 348 3e-05
(0.0204) 		0.00031
(0.192) 		0.145
(1.00) 		0.638
(1.00) 		0.00977
(1.00) 		0.0315
(1.00) 		0.0196
(1.00) 		0.00041
(0.249) 		0.0195
(1.00) 		0.00072
(0.429)
12q loss 38 (10%) 331 1e-05
(0.0079) 		2e-05
(0.0138) 		0.545
(1.00) 		0.114
(1.00) 		0.00338
(1.00) 		0.00581
(1.00) 		0.665
(1.00) 		0.00492
(1.00) 		0.178
(1.00) 		0.00021
(0.133)
21q loss 143 (39%) 226 1e-05
(0.0079) 		0.0232
(1.00) 		0.101
(1.00) 		0.297
(1.00) 		0.0369
(1.00) 		0.00167
(0.92) 		0.00039
(0.238) 		0.00526
(1.00) 		0.00015
(0.0966) 		0.00198
(1.00)
xq gain 44 (12%) 325 1e-05
(0.0079) 		0.00017
(0.109) 		0.748
(1.00) 		0.507
(1.00) 		0.0524
(1.00) 		0.00042
(0.255) 		0.0569
(1.00) 		0.439
(1.00) 		0.125
(1.00) 		0.0469
(1.00)
1p loss 46 (12%) 323 1e-05
(0.0079) 		0.00011
(0.0717) 		0.0593
(1.00) 		0.295
(1.00) 		0.0363
(1.00) 		0.0112
(1.00) 		0.337
(1.00) 		0.0243
(1.00) 		0.129
(1.00) 		0.00571
(1.00)
1q loss 21 (6%) 348 6e-05
(0.04) 		0.00014
(0.0903) 		0.0335
(1.00) 		0.301
(1.00) 		0.565
(1.00) 		0.216
(1.00) 		0.23
(1.00) 		0.316
(1.00) 		0.243
(1.00) 		0.118
(1.00)
2q loss 24 (7%) 345 4e-05
(0.0268) 		8e-05
(0.0526) 		0.729
(1.00) 		0.933
(1.00) 		0.0113
(1.00) 		0.412
(1.00) 		0.123
(1.00) 		0.0152
(1.00) 		0.023
(1.00) 		0.156
(1.00)
3p loss 74 (20%) 295 1e-05
(0.0079) 		0.0174
(1.00) 		0.36
(1.00) 		0.199
(1.00) 		0.00324
(1.00) 		0.0003
(0.186) 		0.00958
(1.00) 		0.00503
(1.00) 		0.0106
(1.00) 		0.00533
(1.00)
5p loss 47 (13%) 322 1e-05
(0.0079) 		0.00297
(1.00) 		0.218
(1.00) 		0.756
(1.00) 		0.00452
(1.00) 		0.0134
(1.00) 		0.00474
(1.00) 		0.00506
(1.00) 		0.00092
(0.541) 		0.00017
(0.109)
7q loss 26 (7%) 343 2e-05
(0.0138) 		0.00265
(1.00) 		0.653
(1.00) 		0.374
(1.00) 		0.0276
(1.00) 		0.189
(1.00) 		0.0462
(1.00) 		0.066
(1.00) 		0.00018
(0.115) 		0.0438
(1.00)
8p loss 65 (18%) 304 1e-05
(0.0079) 		0.0442
(1.00) 		0.399
(1.00) 		0.768
(1.00) 		0.00862
(1.00) 		0.00138
(0.781) 		0.00512
(1.00) 		0.00766
(1.00) 		3e-05
(0.0204) 		0.00095
(0.554)
9q loss 81 (22%) 288 1e-05
(0.0079) 		0.00145
(0.813) 		0.247
(1.00) 		0.0165
(1.00) 		0.00015
(0.0966) 		0.0167
(1.00) 		0.00148
(0.829) 		0.00098
(0.569) 		0.0058
(1.00) 		0.00156
(0.872)
14q loss 88 (24%) 281 1e-05
(0.0079) 		9e-05
(0.0591) 		0.561
(1.00) 		0.531
(1.00) 		0.00111
(0.64) 		0.00691
(1.00) 		0.0365
(1.00) 		0.00143
(0.804) 		0.0134
(1.00) 		0.00467
(1.00)
20p loss 19 (5%) 350 0.00033
(0.203) 		0.00036
(0.22) 		1
(1.00) 		0.37
(1.00) 		0.00044
(0.266) 		0.0574
(1.00) 		0.106
(1.00) 		0.646
(1.00) 		0.436
(1.00) 		0.588
(1.00)
xq loss 43 (12%) 326 1e-05
(0.0079) 		4e-05
(0.0268) 		0.263
(1.00) 		0.0696
(1.00) 		0.0572
(1.00) 		0.158
(1.00) 		0.0458
(1.00) 		0.795
(1.00) 		0.0486
(1.00) 		0.186
(1.00)
1p gain 44 (12%) 325 1e-05
(0.0079) 		0.0522
(1.00) 		0.00534
(1.00) 		0.609
(1.00) 		0.0174
(1.00) 		0.402
(1.00) 		0.0102
(1.00) 		0.0853
(1.00) 		0.00048
(0.289) 		0.0472
(1.00)
2p gain 61 (17%) 308 1e-05
(0.0079) 		0.00624
(1.00) 		0.0216
(1.00) 		0.118
(1.00) 		0.143
(1.00) 		0.0279
(1.00) 		0.00096
(0.559) 		0.0374
(1.00) 		0.00273
(1.00) 		0.00122
(0.699)
2q gain 52 (14%) 317 1e-05
(0.0079) 		0.163
(1.00) 		0.239
(1.00) 		0.557
(1.00) 		0.0448
(1.00) 		0.0299
(1.00) 		0.117
(1.00) 		0.283
(1.00) 		0.101
(1.00) 		0.0584
(1.00)
7p gain 161 (44%) 208 1e-05
(0.0079) 		0.00211
(1.00) 		0.612
(1.00) 		0.833
(1.00) 		0.397
(1.00) 		0.00079
(0.468) 		0.0313
(1.00) 		0.114
(1.00) 		0.0154
(1.00) 		0.00142
(0.799)
7q gain 139 (38%) 230 1e-05
(0.0079) 		0.0384
(1.00) 		0.842
(1.00) 		0.608
(1.00) 		0.508
(1.00) 		0.00772
(1.00) 		0.119
(1.00) 		0.328
(1.00) 		0.286
(1.00) 		0.0459
(1.00)
8p gain 155 (42%) 214 2e-05
(0.0138) 		0.0115
(1.00) 		0.565
(1.00) 		0.392
(1.00) 		0.35
(1.00) 		0.115
(1.00) 		0.283
(1.00) 		0.646
(1.00) 		0.00808
(1.00) 		0.21
(1.00)
8q gain 208 (56%) 161 0.00134
(0.76) 		0.0166
(1.00) 		0.788
(1.00) 		0.299
(1.00) 		0.0256
(1.00) 		0.0199
(1.00) 		0.00523
(1.00) 		0.0275
(1.00) 		0.00023
(0.145) 		0.00341
(1.00)
10q gain 59 (16%) 310 1e-05
(0.0079) 		0.00648
(1.00) 		0.129
(1.00) 		0.743
(1.00) 		0.0201
(1.00) 		0.112
(1.00) 		0.151
(1.00) 		0.147
(1.00) 		0.236
(1.00) 		0.0401
(1.00)
11q gain 53 (14%) 316 1e-05
(0.0079) 		0.00157
(0.874) 		0.837
(1.00) 		1
(1.00) 		0.312
(1.00) 		0.00622
(1.00) 		0.00067
(0.401) 		0.00093
(0.543) 		0.00635
(1.00) 		0.00125
(0.715)
14q gain 23 (6%) 346 0.00035
(0.214) 		0.251
(1.00) 		0.798
(1.00) 		0.646
(1.00) 		0.641
(1.00) 		0.525
(1.00) 		0.00893
(1.00) 		0.637
(1.00) 		0.0363
(1.00) 		0.82
(1.00)
15q gain 31 (8%) 338 6e-05
(0.04) 		0.00211
(1.00) 		0.208
(1.00) 		0.827
(1.00) 		0.02
(1.00) 		0.125
(1.00) 		0.282
(1.00) 		0.268
(1.00) 		0.365
(1.00) 		0.227
(1.00)
2p loss 20 (5%) 349 0.00017
(0.109) 		0.00092
(0.541) 		0.35
(1.00) 		0.535
(1.00) 		0.0155
(1.00) 		0.491
(1.00) 		0.126
(1.00) 		0.164
(1.00) 		0.0667
(1.00) 		0.591
(1.00)
6p loss 43 (12%) 326 1e-05
(0.0079) 		0.00313
(1.00) 		0.15
(1.00) 		0.913
(1.00) 		0.0236
(1.00) 		0.0123
(1.00) 		0.109
(1.00) 		0.00192
(1.00) 		0.0651
(1.00) 		0.00232
(1.00)
6q loss 56 (15%) 313 1e-05
(0.0079) 		0.00191
(1.00) 		0.765
(1.00) 		0.681
(1.00) 		0.0417
(1.00) 		0.126
(1.00) 		0.603
(1.00) 		0.027
(1.00) 		0.326
(1.00) 		0.0717
(1.00)
7p loss 14 (4%) 355 0.00133
(0.755) 		0.0074
(1.00) 		0.443
(1.00) 		0.403
(1.00) 		0.00162
(0.899) 		0.219
(1.00) 		0.188
(1.00) 		0.0177
(1.00) 		0.0003
(0.186) 		0.00244
(1.00)
10p loss 49 (13%) 320 3e-05
(0.0204) 		0.0361
(1.00) 		0.552
(1.00) 		0.0893
(1.00) 		0.015
(1.00) 		0.0735
(1.00) 		0.012
(1.00) 		0.0116
(1.00) 		0.0062
(1.00) 		0.0145
(1.00)
10q loss 55 (15%) 314 1e-05
(0.0079) 		0.0045
(1.00) 		0.609
(1.00) 		0.0318
(1.00) 		0.00092
(0.541) 		0.00256
(1.00) 		0.00868
(1.00) 		0.0191
(1.00) 		0.0129
(1.00) 		0.00112
(0.645)
11p loss 54 (15%) 315 2e-05
(0.0138) 		0.0115
(1.00) 		0.00911
(1.00) 		0.136
(1.00) 		0.0987
(1.00) 		0.198
(1.00) 		0.121
(1.00) 		0.0192
(1.00) 		0.132
(1.00) 		0.00693
(1.00)
13q loss 31 (8%) 338 6e-05
(0.04) 		0.694
(1.00) 		0.686
(1.00) 		0.304
(1.00) 		0.28
(1.00) 		0.601
(1.00) 		0.728
(1.00) 		0.911
(1.00) 		0.335
(1.00) 		0.603
(1.00)
18p loss 107 (29%) 262 1e-05
(0.0079) 		0.631
(1.00) 		0.505
(1.00) 		0.62
(1.00) 		0.394
(1.00) 		0.258
(1.00) 		0.187
(1.00) 		0.422
(1.00) 		0.363
(1.00) 		0.207
(1.00)
18q loss 132 (36%) 237 1e-05
(0.0079) 		0.0267
(1.00) 		0.294
(1.00) 		0.868
(1.00) 		0.00708
(1.00) 		0.0225
(1.00) 		0.00514
(1.00) 		0.00329
(1.00) 		0.014
(1.00) 		0.00129
(0.735)
3p gain 40 (11%) 329 0.00529
(1.00) 		0.0118
(1.00) 		0.791
(1.00) 		0.0255
(1.00) 		0.627
(1.00) 		0.223
(1.00) 		0.612
(1.00) 		0.58
(1.00) 		0.102
(1.00) 		0.344
(1.00)
3q gain 69 (19%) 300 0.0134
(1.00) 		0.317
(1.00) 		0.874
(1.00) 		0.149
(1.00) 		0.168
(1.00) 		0.0292
(1.00) 		0.597
(1.00) 		0.525
(1.00) 		0.165
(1.00) 		0.638
(1.00)
4p gain 13 (4%) 356 0.159
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.448
(1.00) 		0.388
(1.00) 		0.427
(1.00) 		0.135
(1.00) 		0.936
(1.00) 		0.726
(1.00) 		0.541
(1.00)
4q gain 9 (2%) 360 0.759
(1.00) 		0.289
(1.00) 		0.867
(1.00) 		0.186
(1.00) 		0.0916
(1.00) 		0.539
(1.00) 		0.486
(1.00) 		0.455
(1.00) 		0.27
(1.00) 		0.26
(1.00)
5q gain 34 (9%) 335 0.00085
(0.502) 		0.0952
(1.00) 		0.658
(1.00) 		0.106
(1.00) 		0.105
(1.00) 		0.35
(1.00) 		0.69
(1.00) 		0.474
(1.00) 		0.495
(1.00) 		0.471
(1.00)
9p gain 48 (13%) 321 0.097
(1.00) 		1
(1.00) 		0.568
(1.00) 		0.924
(1.00) 		0.373
(1.00) 		0.582
(1.00) 		0.243
(1.00) 		0.827
(1.00) 		0.0691
(1.00) 		0.527
(1.00)
9q gain 61 (17%) 308 0.238
(1.00) 		0.982
(1.00) 		0.246
(1.00) 		0.994
(1.00) 		0.43
(1.00) 		0.927
(1.00) 		0.43
(1.00) 		0.525
(1.00) 		0.503
(1.00) 		0.606
(1.00)
11p gain 45 (12%) 324 0.00121
(0.696) 		0.0408
(1.00) 		0.934
(1.00) 		0.845
(1.00) 		0.283
(1.00) 		0.394
(1.00) 		0.00585
(1.00) 		0.00527
(1.00) 		0.0179
(1.00) 		0.0475
(1.00)
12p gain 77 (21%) 292 0.00289
(1.00) 		0.242
(1.00) 		0.238
(1.00) 		0.337
(1.00) 		0.168
(1.00) 		0.102
(1.00) 		0.00139
(0.784) 		0.323
(1.00) 		0.00702
(1.00) 		0.115
(1.00)
12q gain 66 (18%) 303 0.0558
(1.00) 		0.966
(1.00) 		0.439
(1.00) 		0.422
(1.00) 		0.966
(1.00) 		0.277
(1.00) 		0.0964
(1.00) 		0.544
(1.00) 		0.273
(1.00) 		0.43
(1.00)
16p gain 52 (14%) 317 0.00073
(0.434) 		0.0096
(1.00) 		0.393
(1.00) 		0.113
(1.00) 		0.0733
(1.00) 		0.286
(1.00) 		0.754
(1.00) 		0.834
(1.00) 		0.828
(1.00) 		0.732
(1.00)
16q gain 42 (11%) 327 0.00671
(1.00) 		0.202
(1.00) 		0.673
(1.00) 		0.262
(1.00) 		0.188
(1.00) 		0.624
(1.00) 		0.57
(1.00) 		0.93
(1.00) 		0.32
(1.00) 		0.854
(1.00)
17p gain 21 (6%) 348 0.0373
(1.00) 		0.861
(1.00) 		0.843
(1.00) 		0.774
(1.00) 		0.506
(1.00) 		0.278
(1.00) 		0.472
(1.00) 		0.513
(1.00) 		0.343
(1.00) 		0.589
(1.00)
17q gain 46 (12%) 323 0.00092
(0.541) 		0.212
(1.00) 		0.941
(1.00) 		0.902
(1.00) 		0.531
(1.00) 		0.201
(1.00) 		0.289
(1.00) 		0.662
(1.00) 		0.221
(1.00) 		0.462
(1.00)
18q gain 45 (12%) 324 0.00369
(1.00) 		0.00621
(1.00) 		0.597
(1.00) 		0.237
(1.00) 		0.371
(1.00) 		0.033
(1.00) 		0.0477
(1.00) 		0.0596
(1.00) 		0.131
(1.00) 		0.0922
(1.00)
19p gain 46 (12%) 323 0.0195
(1.00) 		0.929
(1.00) 		0.657
(1.00) 		0.0876
(1.00) 		0.608
(1.00) 		0.908
(1.00) 		0.766
(1.00) 		1
(1.00) 		0.741
(1.00) 		0.458
(1.00)
19q gain 61 (17%) 308 0.00131
(0.745) 		0.361
(1.00) 		0.297
(1.00) 		0.0956
(1.00) 		0.0186
(1.00) 		0.345
(1.00) 		0.184
(1.00) 		0.0324
(1.00) 		0.106
(1.00) 		0.0677
(1.00)
22q gain 28 (8%) 341 0.00063
(0.377) 		0.136
(1.00) 		0.846
(1.00) 		0.218
(1.00) 		0.255
(1.00) 		0.067
(1.00) 		0.243
(1.00) 		0.578
(1.00) 		0.236
(1.00) 		0.415
(1.00)
8q loss 20 (5%) 349 0.0198
(1.00) 		0.423
(1.00) 		0.942
(1.00) 		0.24
(1.00) 		0.7
(1.00) 		0.959
(1.00) 		0.367
(1.00) 		0.631
(1.00) 		0.408
(1.00) 		0.753
(1.00)
11q loss 52 (14%) 317 0.00121
(0.696) 		0.241
(1.00) 		0.529
(1.00) 		0.384
(1.00) 		0.679
(1.00) 		0.606
(1.00) 		0.306
(1.00) 		0.288
(1.00) 		0.103
(1.00) 		0.144
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
1P GAIN MUTATED 4 6 11 2 21
1P GAIN WILD-TYPE 165 27 55 8 70

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
1Q GAIN MUTATED 12 12 18 6 40
1Q GAIN WILD-TYPE 157 21 48 4 51

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
1Q GAIN MUTATED 25 36 16
1Q GAIN WILD-TYPE 95 56 93

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
1Q GAIN MUTATED 11 7 8 9 30
1Q GAIN WILD-TYPE 54 55 38 28 32

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
2P GAIN MUTATED 9 12 16 2 22
2P GAIN WILD-TYPE 160 21 50 8 69

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
2Q GAIN MUTATED 9 12 14 1 16
2Q GAIN WILD-TYPE 160 21 52 9 75

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

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S7.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
5P GAIN MUTATED 14 5 14 1 50
5P GAIN WILD-TYPE 155 28 52 9 41

Figure S7.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S8.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
5P GAIN MUTATED 15 37 18
5P GAIN WILD-TYPE 105 55 91

Figure S8.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S9.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
5P GAIN MUTATED 10 5 7 8 29
5P GAIN WILD-TYPE 55 57 39 29 33

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S10.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
5P GAIN MUTATED 34 10 40
5P GAIN WILD-TYPE 145 73 66

Figure S10.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S11.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
5P GAIN MUTATED 31 4 35
5P GAIN WILD-TYPE 146 58 47

Figure S11.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S12.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
6P GAIN MUTATED 6 7 14 2 40
6P GAIN WILD-TYPE 163 26 52 8 51

Figure S12.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S13.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
6P GAIN MUTATED 14 35 7
6P GAIN WILD-TYPE 106 57 102

Figure S13.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.15

Table S14.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
6P GAIN MUTATED 9 5 6 5 24
6P GAIN WILD-TYPE 56 57 40 32 38

Figure S14.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S15.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
6P GAIN MUTATED 19 8 41
6P GAIN WILD-TYPE 100 100 100

Figure S15.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.084

Table S16.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
6P GAIN MUTATED 7 39 9
6P GAIN WILD-TYPE 70 105 91

Figure S16.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S17.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
6P GAIN MUTATED 26 2 27
6P GAIN WILD-TYPE 151 60 55

Figure S17.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S18.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
6Q GAIN MUTATED 5 5 10 2 33
6Q GAIN WILD-TYPE 164 28 56 8 58

Figure S18.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S19.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
6Q GAIN MUTATED 13 27 5
6Q GAIN WILD-TYPE 107 65 104

Figure S19.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.17

Table S20.  Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
6Q GAIN MUTATED 5 4 5 5 21
6Q GAIN WILD-TYPE 60 58 41 32 41

Figure S20.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S21.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
6Q GAIN MUTATED 14 6 34
6Q GAIN WILD-TYPE 105 102 107

Figure S21.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S22.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
6Q GAIN MUTATED 4 33 7
6Q GAIN WILD-TYPE 73 111 93

Figure S22.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S23.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
7P GAIN MUTATED 42 30 34 7 48
7P GAIN WILD-TYPE 127 3 32 3 43

Figure S23.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S24.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
7Q GAIN MUTATED 41 28 27 6 37
7Q GAIN WILD-TYPE 128 5 39 4 54

Figure S24.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S25.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
8P GAIN MUTATED 75 19 17 10 34
8P GAIN WILD-TYPE 94 14 49 0 57

Figure S25.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S26.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
8Q GAIN MUTATED 39 96 41
8Q GAIN WILD-TYPE 38 48 59

Figure S26.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S27.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
10P GAIN MUTATED 10 8 33 0 34
10P GAIN WILD-TYPE 159 25 33 10 57

Figure S27.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S28.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
10P GAIN MUTATED 20 37 16
10P GAIN WILD-TYPE 100 55 93

Figure S28.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S29.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
10P GAIN MUTATED 31 9 32
10P GAIN WILD-TYPE 146 53 50

Figure S29.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S30.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
10Q GAIN MUTATED 8 3 29 0 19
10Q GAIN WILD-TYPE 161 30 37 10 72

Figure S30.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S31.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
11Q GAIN MUTATED 8 5 16 2 22
11Q GAIN WILD-TYPE 161 28 50 8 69

Figure S31.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S32.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
13Q GAIN MUTATED 34 26 16 4 49
13Q GAIN WILD-TYPE 135 7 50 6 42

Figure S32.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S33.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
13Q GAIN MUTATED 34 48 29
13Q GAIN WILD-TYPE 86 44 80

Figure S33.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S34.  Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
13Q GAIN MUTATED 3 5 16 16 24 19 6
13Q GAIN WILD-TYPE 35 16 33 46 17 21 15

Figure S34.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S35.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
13Q GAIN MUTATED 18 67 25
13Q GAIN WILD-TYPE 59 77 75

Figure S35.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S36.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
13Q GAIN MUTATED 51 15 44
13Q GAIN WILD-TYPE 126 47 38

Figure S36.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S37.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
14Q GAIN MUTATED 4 5 1 1 12
14Q GAIN WILD-TYPE 165 28 65 9 79

Figure S37.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S38.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
15Q GAIN MUTATED 4 2 14 0 11
15Q GAIN WILD-TYPE 165 31 52 10 80

Figure S38.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S39.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
18P GAIN MUTATED 12 4 17 2 31
18P GAIN WILD-TYPE 157 29 49 8 60

Figure S39.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S40.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
18P GAIN MUTATED 12 34 12
18P GAIN WILD-TYPE 108 58 97

Figure S40.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S41.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
18P GAIN MUTATED 15 11 40
18P GAIN WILD-TYPE 104 97 101

Figure S41.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S42.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
18P GAIN MUTATED 24 9 33
18P GAIN WILD-TYPE 155 74 73

Figure S42.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S43.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
20P GAIN MUTATED 55 27 47 7 65
20P GAIN WILD-TYPE 114 6 19 3 26

Figure S43.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.078

Table S44.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
20P GAIN MUTATED 56 67 51
20P GAIN WILD-TYPE 64 25 58

Figure S44.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S45.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
20P GAIN MUTATED 16 19 17 28 28 32 2
20P GAIN WILD-TYPE 22 2 32 34 13 8 19

Figure S45.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S46.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
20P GAIN MUTATED 87 26 60
20P GAIN WILD-TYPE 90 36 22

Figure S46.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S47.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
20Q GAIN MUTATED 63 30 53 8 77
20Q GAIN WILD-TYPE 106 3 13 2 14

Figure S47.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S48.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
20Q GAIN MUTATED 61 81 61
20Q GAIN WILD-TYPE 59 11 48

Figure S48.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S49.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
20Q GAIN MUTATED 30 31 27 24 56
20Q GAIN WILD-TYPE 35 31 19 13 6

Figure S49.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S50.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
20Q GAIN MUTATED 22 19 19 38 31 37 2
20Q GAIN WILD-TYPE 16 2 30 24 10 3 19

Figure S50.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S51.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
20Q GAIN MUTATED 66 57 107
20Q GAIN WILD-TYPE 53 51 34

Figure S51.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S52.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
20Q GAIN MUTATED 97 42 91
20Q GAIN WILD-TYPE 82 41 15

Figure S52.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S53.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
20Q GAIN MUTATED 100 28 74
20Q GAIN WILD-TYPE 77 34 8

Figure S53.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S54.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
21Q GAIN MUTATED 1 1 5 0 14
21Q GAIN WILD-TYPE 168 32 61 10 77

Figure S54.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.19

Table S55.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
21Q GAIN MUTATED 4 14 2
21Q GAIN WILD-TYPE 116 78 107

Figure S55.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.25

Table S56.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
21Q GAIN MUTATED 8 0 13
21Q GAIN WILD-TYPE 171 83 93

Figure S56.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S57.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
XQ GAIN MUTATED 7 11 5 3 18
XQ GAIN WILD-TYPE 162 22 61 7 73

Figure S57.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S58.  Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
XQ GAIN MUTATED 13 21 4
XQ GAIN WILD-TYPE 107 71 105

Figure S58.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S59.  Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
1P LOSS MUTATED 2 4 15 1 24
1P LOSS WILD-TYPE 167 29 51 9 67

Figure S59.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S60.  Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
1P LOSS MUTATED 11 24 6
1P LOSS WILD-TYPE 109 68 103

Figure S60.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S61.  Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
1Q LOSS MUTATED 1 0 8 1 11
1Q LOSS WILD-TYPE 168 33 58 9 80

Figure S61.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.09

Table S62.  Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
1Q LOSS MUTATED 5 14 1
1Q LOSS WILD-TYPE 115 78 108

Figure S62.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S63.  Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
2P LOSS MUTATED 1 1 6 0 12
2P LOSS WILD-TYPE 168 32 60 10 79

Figure S63.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S64.  Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
2Q LOSS MUTATED 1 2 6 0 15
2Q LOSS WILD-TYPE 168 31 60 10 76

Figure S64.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.053

Table S65.  Gene #44: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
2Q LOSS MUTATED 4 15 2
2Q LOSS WILD-TYPE 116 77 107

Figure S65.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S66.  Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
3P LOSS MUTATED 10 14 19 1 30
3P LOSS WILD-TYPE 159 19 47 9 61

Figure S66.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S67.  Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
3P LOSS MUTATED 5 2 4 9 13 15 0
3P LOSS WILD-TYPE 33 19 45 53 28 25 21

Figure S67.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S68.  Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
3Q LOSS MUTATED 4 9 9 1 24
3Q LOSS WILD-TYPE 165 24 57 9 67

Figure S68.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.065

Table S69.  Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
3Q LOSS MUTATED 2 3 2 6 17
3Q LOSS WILD-TYPE 63 59 44 31 45

Figure S69.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S70.  Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
3Q LOSS MUTATED 3 0 1 3 10 13 0
3Q LOSS WILD-TYPE 35 21 48 59 31 27 21

Figure S70.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.2

Table S71.  Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
3Q LOSS MUTATED 3 31 9
3Q LOSS WILD-TYPE 74 113 91

Figure S71.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S72.  Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
4P LOSS MUTATED 22 15 44 3 55
4P LOSS WILD-TYPE 147 18 22 7 36

Figure S72.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S73.  Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
4P LOSS MUTATED 32 53 35
4P LOSS WILD-TYPE 88 39 74

Figure S73.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S74.  Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
4P LOSS MUTATED 11 2 18 17 18 25 3
4P LOSS WILD-TYPE 27 19 31 45 23 15 18

Figure S74.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S75.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
4P LOSS MUTATED 51 26 62
4P LOSS WILD-TYPE 128 57 44

Figure S75.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S76.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
4P LOSS MUTATED 52 18 51
4P LOSS WILD-TYPE 125 44 31

Figure S76.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S77.  Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
4Q LOSS MUTATED 21 14 46 3 53
4Q LOSS WILD-TYPE 148 19 20 7 38

Figure S77.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S78.  Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
4Q LOSS MUTATED 34 55 32
4Q LOSS WILD-TYPE 86 37 77

Figure S78.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S79.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
4Q LOSS MUTATED 51 25 61
4Q LOSS WILD-TYPE 128 58 45

Figure S79.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S80.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
4Q LOSS MUTATED 54 18 50
4Q LOSS WILD-TYPE 123 44 32

Figure S80.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S81.  Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
5P LOSS MUTATED 4 8 14 4 17
5P LOSS WILD-TYPE 165 25 52 6 74

Figure S81.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S82.  Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
5P LOSS MUTATED 19 2 22
5P LOSS WILD-TYPE 158 60 60

Figure S82.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S83.  Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
5Q LOSS MUTATED 6 11 19 5 40
5Q LOSS WILD-TYPE 163 22 47 5 51

Figure S83.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S84.  Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
5Q LOSS MUTATED 19 42 13
5Q LOSS WILD-TYPE 101 50 96

Figure S84.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S85.  Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
5Q LOSS MUTATED 11 3 5 7 28
5Q LOSS WILD-TYPE 54 59 41 30 34

Figure S85.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S86.  Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
5Q LOSS MUTATED 6 3 2 13 8 20 2
5Q LOSS WILD-TYPE 32 18 47 49 33 20 19

Figure S86.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S87.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
5Q LOSS MUTATED 20 12 49
5Q LOSS WILD-TYPE 99 96 92

Figure S87.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S88.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
5Q LOSS MUTATED 28 9 44
5Q LOSS WILD-TYPE 151 74 62

Figure S88.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S89.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
5Q LOSS MUTATED 12 51 12
5Q LOSS WILD-TYPE 65 93 88

Figure S89.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S90.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
5Q LOSS MUTATED 27 4 44
5Q LOSS WILD-TYPE 150 58 38

Figure S90.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S91.  Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
6P LOSS MUTATED 4 4 19 0 16
6P LOSS WILD-TYPE 165 29 47 10 75

Figure S91.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S92.  Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
6Q LOSS MUTATED 8 5 24 0 19
6Q LOSS WILD-TYPE 161 28 42 10 72

Figure S92.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S93.  Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
7P LOSS MUTATED 0 11 0
7P LOSS WILD-TYPE 77 133 100

Figure S93.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S94.  Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
7Q LOSS MUTATED 1 1 9 1 14
7Q LOSS WILD-TYPE 168 32 57 9 77

Figure S94.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S95.  Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
7Q LOSS MUTATED 1 20 2
7Q LOSS WILD-TYPE 76 124 98

Figure S95.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S96.  Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
8P LOSS MUTATED 9 6 24 0 26
8P LOSS WILD-TYPE 160 27 42 10 65

Figure S96.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S97.  Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
8P LOSS MUTATED 10 41 7
8P LOSS WILD-TYPE 67 103 93

Figure S97.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S98.  Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
9P LOSS MUTATED 12 13 48 4 39
9P LOSS WILD-TYPE 157 20 18 6 52

Figure S98.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S99.  Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
9P LOSS MUTATED 26 50 28
9P LOSS WILD-TYPE 94 42 81

Figure S99.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S100.  Gene #57: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 83 55 91
9P LOSS MUTATED 6 36 7 32
9P LOSS WILD-TYPE 28 47 48 59

Figure S100.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S101.  Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
9P LOSS MUTATED 6 13 19 9 35
9P LOSS WILD-TYPE 59 49 27 28 27

Figure S101.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.084

Table S102.  Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
9P LOSS MUTATED 13 1 10 23 13 21 1
9P LOSS WILD-TYPE 25 20 39 39 28 19 20

Figure S102.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S103.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
9P LOSS MUTATED 40 23 52
9P LOSS WILD-TYPE 139 60 54

Figure S103.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.065

Table S104.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
9P LOSS MUTATED 46 15 43
9P LOSS WILD-TYPE 131 47 39

Figure S104.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S105.  Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
9Q LOSS MUTATED 11 10 30 3 27
9Q LOSS WILD-TYPE 158 23 36 7 64

Figure S105.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S106.  Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
9Q LOSS MUTATED 6 10 13 4 25
9Q LOSS WILD-TYPE 59 52 33 33 37

Figure S106.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S107.  Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
10P LOSS MUTATED 7 7 10 1 24
10P LOSS WILD-TYPE 162 26 56 9 67

Figure S107.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S108.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
10Q LOSS MUTATED 6 10 8 2 29
10Q LOSS WILD-TYPE 163 23 58 8 62

Figure S108.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S109.  Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
11P LOSS MUTATED 9 4 15 0 26
11P LOSS WILD-TYPE 160 29 51 10 65

Figure S109.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S110.  Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
12P LOSS MUTATED 1 2 11 1 33
12P LOSS WILD-TYPE 168 31 55 9 58

Figure S110.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S111.  Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
12P LOSS MUTATED 3 29 6
12P LOSS WILD-TYPE 117 63 103

Figure S111.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.059

Table S112.  Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
12P LOSS MUTATED 3 4 6 3 20
12P LOSS WILD-TYPE 62 58 40 34 42

Figure S112.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S113.  Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
12P LOSS MUTATED 2 0 3 10 4 17 0
12P LOSS WILD-TYPE 36 21 46 52 37 23 21

Figure S113.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S114.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
12P LOSS MUTATED 13 6 29
12P LOSS WILD-TYPE 166 77 77

Figure S114.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S115.  Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
12P LOSS MUTATED 10 3 25
12P LOSS WILD-TYPE 167 59 57

Figure S115.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S116.  Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
12Q LOSS MUTATED 0 2 10 1 25
12Q LOSS WILD-TYPE 169 31 56 9 66

Figure S116.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S117.  Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
12Q LOSS MUTATED 4 22 5
12Q LOSS WILD-TYPE 116 70 104

Figure S117.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S118.  Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
12Q LOSS MUTATED 10 3 18
12Q LOSS WILD-TYPE 167 59 64

Figure S118.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S119.  Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
13Q LOSS MUTATED 7 0 16 1 7
13Q LOSS WILD-TYPE 162 33 50 9 84

Figure S119.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S120.  Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
14Q LOSS MUTATED 17 7 30 2 32
14Q LOSS WILD-TYPE 152 26 36 8 59

Figure S120.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.059

Table S121.  Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
14Q LOSS MUTATED 20 38 19
14Q LOSS WILD-TYPE 100 54 90

Figure S121.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S122.  Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
15Q LOSS MUTATED 10 12 21 3 32
15Q LOSS WILD-TYPE 159 21 45 7 59

Figure S122.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S123.  Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
15Q LOSS MUTATED 8 4 9 4 23
15Q LOSS WILD-TYPE 57 58 37 33 39

Figure S123.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.19

Table S124.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
15Q LOSS MUTATED 33 9 36
15Q LOSS WILD-TYPE 146 74 70

Figure S124.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.19

Table S125.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
15Q LOSS MUTATED 11 47 13
15Q LOSS WILD-TYPE 66 97 87

Figure S125.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S126.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
15Q LOSS MUTATED 35 5 31
15Q LOSS WILD-TYPE 142 57 51

Figure S126.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S127.  Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
16P LOSS MUTATED 8 3 24 0 42
16P LOSS WILD-TYPE 161 30 42 10 49

Figure S127.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.22

Table S128.  Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
16P LOSS MUTATED 18 33 16
16P LOSS WILD-TYPE 102 59 93

Figure S128.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S129.  Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
16P LOSS MUTATED 7 5 5 4 31
16P LOSS WILD-TYPE 58 57 41 33 31

Figure S129.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S130.  Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
16P LOSS MUTATED 7 0 4 9 8 21 3
16P LOSS WILD-TYPE 31 21 45 53 33 19 18

Figure S130.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S131.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
16P LOSS MUTATED 13 16 48
16P LOSS WILD-TYPE 106 92 93

Figure S131.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.059

Table S132.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
16P LOSS MUTATED 27 12 38
16P LOSS WILD-TYPE 152 71 68

Figure S132.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S133.  Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
16P LOSS MUTATED 6 48 14
16P LOSS WILD-TYPE 71 96 86

Figure S133.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S134.  Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
16P LOSS MUTATED 29 6 33
16P LOSS WILD-TYPE 148 56 49

Figure S134.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S135.  Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
16Q LOSS MUTATED 12 3 24 2 45
16Q LOSS WILD-TYPE 157 30 42 8 46

Figure S135.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S136.  Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
16Q LOSS MUTATED 14 38 22
16Q LOSS WILD-TYPE 106 54 87

Figure S136.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S137.  Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
16Q LOSS MUTATED 6 10 10 5 32
16Q LOSS WILD-TYPE 59 52 36 32 30

Figure S137.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S138.  Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
16Q LOSS MUTATED 8 0 8 14 8 23 2
16Q LOSS WILD-TYPE 30 21 41 48 33 17 19

Figure S138.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S139.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
16Q LOSS MUTATED 17 20 49
16Q LOSS WILD-TYPE 102 88 92

Figure S139.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.15

Table S140.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
16Q LOSS MUTATED 30 16 40
16Q LOSS WILD-TYPE 149 67 66

Figure S140.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S141.  Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
16Q LOSS MUTATED 31 9 35
16Q LOSS WILD-TYPE 146 53 47

Figure S141.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S142.  Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
17P LOSS MUTATED 12 21 37 3 58
17P LOSS WILD-TYPE 157 12 29 7 33

Figure S142.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S143.  Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
17P LOSS MUTATED 34 60 21
17P LOSS WILD-TYPE 86 32 88

Figure S143.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S144.  Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
17P LOSS MUTATED 14 10 18 12 37
17P LOSS WILD-TYPE 51 52 28 25 25

Figure S144.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S145.  Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
17P LOSS MUTATED 14 2 7 22 17 27 2
17P LOSS WILD-TYPE 24 19 42 40 24 13 19

Figure S145.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S146.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
17P LOSS MUTATED 40 24 66
17P LOSS WILD-TYPE 79 84 75

Figure S146.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S147.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
17P LOSS MUTATED 57 18 55
17P LOSS WILD-TYPE 122 65 51

Figure S147.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S148.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
17P LOSS MUTATED 22 71 22
17P LOSS WILD-TYPE 55 73 78

Figure S148.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S149.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
17P LOSS MUTATED 56 10 49
17P LOSS WILD-TYPE 121 52 33

Figure S149.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S150.  Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
17Q LOSS MUTATED 5 7 17 2 30
17Q LOSS WILD-TYPE 164 26 49 8 61

Figure S150.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S151.  Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
17Q LOSS MUTATED 13 29 8
17Q LOSS WILD-TYPE 107 63 101

Figure S151.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.21

Table S152.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
17Q LOSS MUTATED 24 6 30
17Q LOSS WILD-TYPE 155 77 76

Figure S152.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S153.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
17Q LOSS MUTATED 19 4 27
17Q LOSS WILD-TYPE 158 58 55

Figure S153.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S154.  Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
18P LOSS MUTATED 27 15 30 2 33
18P LOSS WILD-TYPE 142 18 36 8 58

Figure S154.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S155.  Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
18Q LOSS MUTATED 29 16 36 2 49
18Q LOSS WILD-TYPE 140 17 30 8 42

Figure S155.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S156.  Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
19P LOSS MUTATED 3 9 23 4 54
19P LOSS WILD-TYPE 166 24 43 6 37

Figure S156.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S157.  Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
19P LOSS MUTATED 19 51 12
19P LOSS WILD-TYPE 101 41 97

Figure S157.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S158.  Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
19P LOSS MUTATED 8 3 8 4 34
19P LOSS WILD-TYPE 57 59 38 33 28

Figure S158.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S159.  Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
19P LOSS MUTATED 5 2 3 14 10 23 0
19P LOSS WILD-TYPE 33 19 46 48 31 17 21

Figure S159.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S160.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
19P LOSS MUTATED 21 12 59
19P LOSS WILD-TYPE 98 96 82

Figure S160.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S161.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
19P LOSS MUTATED 29 8 55
19P LOSS WILD-TYPE 150 75 51

Figure S161.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S162.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
19P LOSS MUTATED 12 58 11
19P LOSS WILD-TYPE 65 86 89

Figure S162.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S163.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
19P LOSS MUTATED 32 5 44
19P LOSS WILD-TYPE 145 57 38

Figure S163.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S164.  Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
19Q LOSS MUTATED 2 7 17 4 42
19Q LOSS WILD-TYPE 167 26 49 6 49

Figure S164.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S165.  Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
19Q LOSS MUTATED 15 39 8
19Q LOSS WILD-TYPE 105 53 101

Figure S165.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S166.  Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
19Q LOSS MUTATED 5 2 8 5 25
19Q LOSS WILD-TYPE 60 60 38 32 37

Figure S166.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S167.  Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
19Q LOSS MUTATED 3 1 2 13 9 17 0
19Q LOSS WILD-TYPE 35 20 47 49 32 23 21

Figure S167.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S168.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
19Q LOSS MUTATED 17 8 47
19Q LOSS WILD-TYPE 102 100 94

Figure S168.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S169.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
19Q LOSS MUTATED 23 7 42
19Q LOSS WILD-TYPE 156 76 64

Figure S169.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S170.  Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
19Q LOSS MUTATED 12 45 6
19Q LOSS WILD-TYPE 65 99 94

Figure S170.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S171.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
19Q LOSS MUTATED 25 4 34
19Q LOSS WILD-TYPE 152 58 48

Figure S171.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.2

Table S172.  Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
20P LOSS MUTATED 1 1 8 0 9
20P LOSS WILD-TYPE 168 32 58 10 82

Figure S172.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.22

Table S173.  Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
20P LOSS MUTATED 1 12 4
20P LOSS WILD-TYPE 119 80 105

Figure S173.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S174.  Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
21Q LOSS MUTATED 28 16 44 7 48
21Q LOSS WILD-TYPE 141 17 22 3 43

Figure S174.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.24

Table S175.  Gene #77: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
21Q LOSS MUTATED 37 33 73
21Q LOSS WILD-TYPE 82 75 68

Figure S175.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S176.  Gene #77: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
21Q LOSS MUTATED 21 75 30
21Q LOSS WILD-TYPE 56 69 70

Figure S176.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S177.  Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
22Q LOSS MUTATED 13 10 38 5 50
22Q LOSS WILD-TYPE 156 23 28 5 41

Figure S177.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S178.  Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
22Q LOSS MUTATED 30 49 24
22Q LOSS WILD-TYPE 90 43 85

Figure S178.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S179.  Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
22Q LOSS MUTATED 23 27 65
22Q LOSS WILD-TYPE 96 81 76

Figure S179.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S180.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
22Q LOSS MUTATED 40 19 56
22Q LOSS WILD-TYPE 139 64 50

Figure S180.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.24

Table S181.  Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
22Q LOSS MUTATED 15 62 25
22Q LOSS WILD-TYPE 62 82 75

Figure S181.  Get High-res Image Gene #78: '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 = 0.0079

Table S182.  Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
22Q LOSS MUTATED 45 11 46
22Q LOSS WILD-TYPE 132 51 36

Figure S182.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S183.  Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
XQ LOSS MUTATED 4 5 17 1 16
XQ LOSS WILD-TYPE 165 28 49 9 75

Figure S183.  Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S184.  Gene #79: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
XQ LOSS MUTATED 15 18 2
XQ LOSS WILD-TYPE 105 74 107

Figure S184.  Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 369

  • Number of significantly arm-level cnvs = 79

  • 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)
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