Correlation between copy number variations of arm-level result and molecular subtypes
Sarcoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1765D8R
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/C1765D8R
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 80 arm-level events and 8 molecular subtypes across 257 patients, 69 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'METHLYATION_CNMF'.

  • 2p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 3p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 4p gain cnv correlated to 'METHLYATION_CNMF'.

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

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7q gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

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

  • 20q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 2p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 19p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 69 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
10q loss 131 (51%) 126 1e-05
(0.0064) 		1e-05
(0.0064) 		1e-05
(0.0064) 		1e-05
(0.0064) 		1e-05
(0.0064) 		1e-05
(0.0064) 		4e-05
(0.0243) 		0.00018
(0.106)
2p loss 88 (34%) 169 1e-05
(0.0064) 		1e-05
(0.0064) 		5e-05
(0.0302) 		0.00015
(0.0888) 		0.00443
(1.00) 		3e-05
(0.0183) 		0.00048
(0.273) 		0.00059
(0.332)
5p gain 98 (38%) 159 1e-05
(0.0064) 		0.0001
(0.0597) 		0.00019
(0.111) 		2e-05
(0.0123) 		0.608
(1.00) 		0.00193
(1.00) 		0.577
(1.00) 		0.483
(1.00)
16q loss 124 (48%) 133 1e-05
(0.0064) 		0.00015
(0.0888) 		0.00128
(0.694) 		0.0014
(0.756) 		0.0154
(1.00) 		0.00023
(0.134) 		0.00015
(0.0888) 		0.00045
(0.256)
xq loss 95 (37%) 162 1e-05
(0.0064) 		2e-05
(0.0123) 		4e-05
(0.0243) 		0.00026
(0.151) 		0.00065
(0.362) 		0.00132
(0.714) 		0.125
(1.00) 		0.0448
(1.00)
3p gain 39 (15%) 218 0.00496
(1.00) 		0.00032
(0.185) 		1e-05
(0.0064) 		0.00022
(0.128) 		0.0754
(1.00) 		0.0192
(1.00) 		0.00339
(1.00) 		0.001
(0.549)
9q gain 73 (28%) 184 1e-05
(0.0064) 		0.00043
(0.246) 		0.00049
(0.278) 		2e-05
(0.0123) 		0.0396
(1.00) 		0.00155
(0.829) 		0.0177
(1.00) 		0.00449
(1.00)
19q gain 65 (25%) 192 1e-05
(0.0064) 		0.00016
(0.0942) 		0.00064
(0.357) 		1e-05
(0.0064) 		0.65
(1.00) 		0.112
(1.00) 		0.874
(1.00) 		0.0174
(1.00)
3p loss 56 (22%) 201 0.0339
(1.00) 		4e-05
(0.0243) 		0.00012
(0.0715) 		0.00034
(0.195) 		0.00111
(0.606) 		0.0148
(1.00) 		0.00092
(0.506) 		0.00044
(0.251)
6p gain 51 (20%) 206 0.00062
(0.347) 		3e-05
(0.0183) 		0.00047
(0.267) 		0.00014
(0.083) 		0.0972
(1.00) 		0.0304
(1.00) 		0.482
(1.00) 		0.029
(1.00)
6q gain 50 (19%) 207 4e-05
(0.0243) 		5e-05
(0.0302) 		0.00091
(0.502) 		0.00058
(0.327) 		0.0616
(1.00) 		0.00516
(1.00) 		0.289
(1.00) 		0.028
(1.00)
20q gain 83 (32%) 174 0.00012
(0.0715) 		0.00118
(0.641) 		0.00031
(0.179) 		0.0165
(1.00) 		0.397
(1.00) 		0.00573
(1.00) 		0.0886
(1.00) 		0.0311
(1.00)
11p loss 94 (37%) 163 1e-05
(0.0064) 		0.00037
(0.212) 		0.213
(1.00) 		0.254
(1.00) 		0.577
(1.00) 		0.48
(1.00) 		0.692
(1.00) 		0.144
(1.00)
11q loss 91 (35%) 166 1e-05
(0.0064) 		0.00032
(0.185) 		0.129
(1.00) 		0.065
(1.00) 		0.535
(1.00) 		0.833
(1.00) 		0.947
(1.00) 		0.0072
(1.00)
13q loss 132 (51%) 125 1e-05
(0.0064) 		0.00643
(1.00) 		0.00012
(0.0715) 		0.00232
(1.00) 		0.329
(1.00) 		0.142
(1.00) 		0.164
(1.00) 		0.279
(1.00)
1p gain 56 (22%) 201 0.00733
(1.00) 		2e-05
(0.0123) 		0.00153
(0.82) 		0.0357
(1.00) 		0.306
(1.00) 		0.476
(1.00) 		0.123
(1.00) 		0.242
(1.00)
2p gain 22 (9%) 235 0.0787
(1.00) 		0.0116
(1.00) 		8e-05
(0.0478) 		0.00903
(1.00) 		0.126
(1.00) 		0.0263
(1.00) 		0.0187
(1.00) 		0.00299
(1.00)
3q gain 36 (14%) 221 0.0446
(1.00) 		0.0123
(1.00) 		7e-05
(0.0421) 		0.00604
(1.00) 		0.0922
(1.00) 		0.00946
(1.00) 		0.00403
(1.00) 		0.00117
(0.636)
4p gain 68 (26%) 189 0.00222
(1.00) 		0.00033
(0.19) 		0.00274
(1.00) 		0.00183
(0.968) 		0.0319
(1.00) 		0.0459
(1.00) 		0.366
(1.00) 		0.103
(1.00)
5q gain 71 (28%) 186 6e-05
(0.0361) 		0.056
(1.00) 		0.0263
(1.00) 		0.00427
(1.00) 		0.362
(1.00) 		0.218
(1.00) 		0.699
(1.00) 		0.791
(1.00)
7q gain 68 (26%) 189 0.0281
(1.00) 		0.00151
(0.812) 		0.00174
(0.926) 		0.018
(1.00) 		0.0976
(1.00) 		0.339
(1.00) 		0.00016
(0.0942) 		0.00654
(1.00)
9p gain 57 (22%) 200 1e-05
(0.0064) 		0.00964
(1.00) 		0.0118
(1.00) 		0.00245
(1.00) 		0.0769
(1.00) 		0.0092
(1.00) 		0.66
(1.00) 		0.469
(1.00)
12p gain 43 (17%) 214 0.126
(1.00) 		0.0365
(1.00) 		0.00021
(0.123) 		0.00076
(0.421) 		0.17
(1.00) 		0.0727
(1.00) 		0.0407
(1.00) 		0.00053
(0.299)
15q gain 63 (25%) 194 7e-05
(0.0421) 		0.0459
(1.00) 		0.0423
(1.00) 		0.147
(1.00) 		0.135
(1.00) 		0.192
(1.00) 		0.0149
(1.00) 		0.0291
(1.00)
17p gain 61 (24%) 196 0.00021
(0.123) 		0.0134
(1.00) 		0.014
(1.00) 		0.00866
(1.00) 		0.11
(1.00) 		0.00854
(1.00) 		0.0604
(1.00) 		0.0523
(1.00)
17q gain 57 (22%) 200 3e-05
(0.0183) 		0.0303
(1.00) 		0.0133
(1.00) 		0.00271
(1.00) 		0.0421
(1.00) 		0.0202
(1.00) 		0.00374
(1.00) 		0.0221
(1.00)
19p gain 87 (34%) 170 1e-05
(0.0064) 		0.0369
(1.00) 		0.0507
(1.00) 		0.00796
(1.00) 		0.565
(1.00) 		0.223
(1.00) 		0.909
(1.00) 		0.0834
(1.00)
21q gain 58 (23%) 199 1e-05
(0.0064) 		0.0316
(1.00) 		0.494
(1.00) 		0.494
(1.00) 		0.98
(1.00) 		0.792
(1.00) 		0.353
(1.00) 		0.554
(1.00)
22q gain 60 (23%) 197 0.433
(1.00) 		0.00437
(1.00) 		0.00033
(0.19) 		0.0135
(1.00) 		0.571
(1.00) 		0.0824
(1.00) 		0.183
(1.00) 		0.0831
(1.00)
2q loss 71 (28%) 186 1e-05
(0.0064) 		0.0833
(1.00) 		0.277
(1.00) 		0.199
(1.00) 		0.824
(1.00) 		0.016
(1.00) 		0.639
(1.00) 		0.559
(1.00)
10p loss 120 (47%) 137 1e-05
(0.0064) 		0.00706
(1.00) 		0.129
(1.00) 		0.0162
(1.00) 		0.118
(1.00) 		0.0324
(1.00) 		0.134
(1.00) 		0.762
(1.00)
12p loss 65 (25%) 192 1e-05
(0.0064) 		0.0073
(1.00) 		0.0867
(1.00) 		0.00647
(1.00) 		1
(1.00) 		0.761
(1.00) 		0.913
(1.00) 		0.413
(1.00)
14q loss 61 (24%) 196 2e-05
(0.0123) 		0.00689
(1.00) 		0.423
(1.00) 		0.00177
(0.94) 		0.637
(1.00) 		0.0583
(1.00) 		0.44
(1.00) 		0.0513
(1.00)
19p loss 21 (8%) 236 0.00408
(1.00) 		0.00574
(1.00) 		0.0002
(0.117) 		0.0295
(1.00) 		0.56
(1.00) 		0.818
(1.00) 		0.573
(1.00) 		0.0325
(1.00)
22q loss 66 (26%) 191 7e-05
(0.0421) 		0.114
(1.00) 		0.524
(1.00) 		0.0421
(1.00) 		0.223
(1.00) 		0.6
(1.00) 		0.1
(1.00) 		0.293
(1.00)
1q gain 49 (19%) 208 0.0133
(1.00) 		0.00652
(1.00) 		0.00463
(1.00) 		0.124
(1.00) 		0.0487
(1.00) 		0.0926
(1.00) 		0.001
(0.549) 		0.00466
(1.00)
2q gain 22 (9%) 235 0.0253
(1.00) 		0.0728
(1.00) 		0.00293
(1.00) 		0.0537
(1.00) 		0.198
(1.00) 		0.0476
(1.00) 		0.0317
(1.00) 		0.164
(1.00)
4q gain 47 (18%) 210 0.0555
(1.00) 		0.0479
(1.00) 		0.0435
(1.00) 		0.0745
(1.00) 		0.367
(1.00) 		0.059
(1.00) 		0.236
(1.00) 		0.411
(1.00)
7p gain 82 (32%) 175 0.00088
(0.487) 		0.00257
(1.00) 		0.00287
(1.00) 		0.0248
(1.00) 		0.301
(1.00) 		0.311
(1.00) 		0.0023
(1.00) 		0.00439
(1.00)
8p gain 52 (20%) 205 0.0552
(1.00) 		0.687
(1.00) 		0.21
(1.00) 		0.154
(1.00) 		0.383
(1.00) 		0.297
(1.00) 		0.297
(1.00) 		0.123
(1.00)
8q gain 65 (25%) 192 0.207
(1.00) 		0.0679
(1.00) 		0.00335
(1.00) 		0.129
(1.00) 		0.273
(1.00) 		0.271
(1.00) 		0.082
(1.00) 		0.118
(1.00)
10p gain 23 (9%) 234 0.0477
(1.00) 		0.047
(1.00) 		0.0725
(1.00) 		0.146
(1.00) 		0.273
(1.00) 		0.706
(1.00) 		0.0232
(1.00) 		0.155
(1.00)
10q gain 12 (5%) 245 0.473
(1.00) 		0.0483
(1.00) 		0.301
(1.00) 		0.523
(1.00) 		0.36
(1.00) 		0.202
(1.00) 		0.0396
(1.00) 		0.313
(1.00)
11p gain 23 (9%) 234 0.18
(1.00) 		0.078
(1.00) 		0.0354
(1.00) 		0.0318
(1.00) 		0.573
(1.00) 		0.144
(1.00) 		0.107
(1.00) 		0.501
(1.00)
11q gain 22 (9%) 235 0.0241
(1.00) 		0.264
(1.00) 		0.0708
(1.00) 		0.093
(1.00) 		1
(1.00) 		0.42
(1.00) 		0.312
(1.00) 		0.748
(1.00)
12q gain 34 (13%) 223 0.167
(1.00) 		0.0599
(1.00) 		0.0135
(1.00) 		0.0619
(1.00) 		0.0559
(1.00) 		0.0779
(1.00) 		0.0618
(1.00) 		0.0131
(1.00)
13q gain 15 (6%) 242 0.22
(1.00) 		0.275
(1.00) 		0.296
(1.00) 		0.293
(1.00) 		0.551
(1.00) 		0.768
(1.00) 		0.616
(1.00) 		0.297
(1.00)
14q gain 57 (22%) 200 0.164
(1.00) 		0.114
(1.00) 		0.0109
(1.00) 		0.05
(1.00) 		0.577
(1.00) 		0.738
(1.00) 		0.332
(1.00) 		0.679
(1.00)
16p gain 40 (16%) 217 0.00209
(1.00) 		0.184
(1.00) 		0.492
(1.00) 		0.306
(1.00) 		0.877
(1.00) 		0.266
(1.00) 		0.891
(1.00) 		0.439
(1.00)
16q gain 21 (8%) 236 0.331
(1.00) 		0.216
(1.00) 		0.0857
(1.00) 		0.117
(1.00) 		0.793
(1.00) 		1
(1.00) 		0.777
(1.00) 		0.061
(1.00)
18p gain 53 (21%) 204 0.0007
(0.389) 		0.0737
(1.00) 		0.249
(1.00) 		0.396
(1.00) 		0.585
(1.00) 		0.213
(1.00) 		0.64
(1.00) 		0.263
(1.00)
18q gain 36 (14%) 221 0.0312
(1.00) 		0.0505
(1.00) 		0.16
(1.00) 		0.245
(1.00) 		0.61
(1.00) 		0.176
(1.00) 		0.254
(1.00) 		0.989
(1.00)
20p gain 62 (24%) 195 0.00091
(0.502) 		0.0908
(1.00) 		0.428
(1.00) 		0.0489
(1.00) 		0.826
(1.00) 		0.11
(1.00) 		0.45
(1.00) 		0.494
(1.00)
xq gain 34 (13%) 223 0.591
(1.00) 		0.0433
(1.00) 		0.167
(1.00) 		0.256
(1.00) 		0.131
(1.00) 		0.567
(1.00) 		0.197
(1.00) 		0.319
(1.00)
1p loss 32 (12%) 225 0.174
(1.00) 		0.0777
(1.00) 		0.675
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.41
(1.00) 		0.688
(1.00)
1q loss 40 (16%) 217 0.15
(1.00) 		0.00704
(1.00) 		0.0904
(1.00) 		0.138
(1.00) 		0.0464
(1.00) 		0.0182
(1.00) 		0.074
(1.00) 		0.0572
(1.00)
3q loss 49 (19%) 208 0.0595
(1.00) 		0.00639
(1.00) 		0.0352
(1.00) 		0.0685
(1.00) 		0.0366
(1.00) 		0.0685
(1.00) 		0.0113
(1.00) 		0.0476
(1.00)
4p loss 42 (16%) 215 0.0217
(1.00) 		0.83
(1.00) 		0.973
(1.00) 		0.988
(1.00) 		0.275
(1.00) 		0.768
(1.00) 		0.905
(1.00) 		0.416
(1.00)
4q loss 51 (20%) 206 0.0102
(1.00) 		0.131
(1.00) 		0.931
(1.00) 		0.939
(1.00) 		0.783
(1.00) 		0.835
(1.00) 		0.899
(1.00) 		0.612
(1.00)
5p loss 22 (9%) 235 0.279
(1.00) 		0.021
(1.00) 		0.0752
(1.00) 		0.0422
(1.00) 		0.355
(1.00) 		0.604
(1.00) 		0.162
(1.00) 		0.236
(1.00)
5q loss 35 (14%) 222 0.034
(1.00) 		0.104
(1.00) 		0.117
(1.00) 		0.0682
(1.00) 		0.971
(1.00) 		0.0444
(1.00) 		0.398
(1.00) 		0.33
(1.00)
6p loss 60 (23%) 197 0.00059
(0.332) 		0.0647
(1.00) 		0.134
(1.00) 		0.285
(1.00) 		0.233
(1.00) 		0.597
(1.00) 		0.395
(1.00) 		0.138
(1.00)
6q loss 53 (21%) 204 0.00151
(0.812) 		0.0106
(1.00) 		0.0805
(1.00) 		0.0903
(1.00) 		0.561
(1.00) 		0.528
(1.00) 		0.656
(1.00) 		0.631
(1.00)
7p loss 32 (12%) 225 0.0263
(1.00) 		0.0109
(1.00) 		0.0511
(1.00) 		0.0464
(1.00) 		0.184
(1.00) 		0.354
(1.00) 		0.259
(1.00) 		0.0262
(1.00)
7q loss 34 (13%) 223 0.00062
(0.347) 		0.196
(1.00) 		0.326
(1.00) 		0.0538
(1.00) 		0.354
(1.00) 		0.385
(1.00) 		0.295
(1.00) 		0.467
(1.00)
8p loss 62 (24%) 195 0.013
(1.00) 		0.00164
(0.876) 		0.336
(1.00) 		0.0888
(1.00) 		0.267
(1.00) 		0.086
(1.00) 		0.195
(1.00) 		0.115
(1.00)
8q loss 46 (18%) 211 0.00286
(1.00) 		0.0005
(0.283) 		0.0321
(1.00) 		0.0446
(1.00) 		0.433
(1.00) 		0.00764
(1.00) 		0.851
(1.00) 		0.136
(1.00)
9p loss 83 (32%) 174 0.314
(1.00) 		0.207
(1.00) 		0.155
(1.00) 		0.0706
(1.00) 		0.505
(1.00) 		0.614
(1.00) 		0.165
(1.00) 		0.236
(1.00)
9q loss 51 (20%) 206 0.188
(1.00) 		0.259
(1.00) 		0.232
(1.00) 		0.0834
(1.00) 		0.781
(1.00) 		0.958
(1.00) 		0.728
(1.00) 		0.451
(1.00)
12q loss 54 (21%) 203 0.00477
(1.00) 		0.0466
(1.00) 		0.252
(1.00) 		0.0493
(1.00) 		0.776
(1.00) 		0.654
(1.00) 		0.556
(1.00) 		0.51
(1.00)
15q loss 45 (18%) 212 0.0158
(1.00) 		0.0539
(1.00) 		0.182
(1.00) 		0.0699
(1.00) 		0.0633
(1.00) 		0.00425
(1.00) 		0.0262
(1.00) 		0.111
(1.00)
16p loss 75 (29%) 182 0.00164
(0.876) 		0.0165
(1.00) 		0.0759
(1.00) 		0.284
(1.00) 		0.161
(1.00) 		0.269
(1.00) 		0.122
(1.00) 		0.543
(1.00)
17p loss 57 (22%) 200 0.0255
(1.00) 		0.352
(1.00) 		0.118
(1.00) 		0.0824
(1.00) 		0.239
(1.00) 		0.272
(1.00) 		0.257
(1.00) 		0.309
(1.00)
17q loss 48 (19%) 209 0.0101
(1.00) 		0.12
(1.00) 		0.467
(1.00) 		0.131
(1.00) 		0.45
(1.00) 		0.239
(1.00) 		0.404
(1.00) 		0.606
(1.00)
18p loss 62 (24%) 195 0.00073
(0.405) 		0.226
(1.00) 		0.18
(1.00) 		0.683
(1.00) 		0.908
(1.00) 		0.143
(1.00) 		0.408
(1.00) 		0.382
(1.00)
18q loss 72 (28%) 185 0.00056
(0.316) 		0.0257
(1.00) 		0.00107
(0.585) 		0.0531
(1.00) 		0.433
(1.00) 		0.176
(1.00) 		0.168
(1.00) 		0.011
(1.00)
19q loss 38 (15%) 219 0.00145
(0.782) 		0.0341
(1.00) 		0.00111
(0.606) 		0.382
(1.00) 		0.946
(1.00) 		0.731
(1.00) 		0.454
(1.00) 		0.162
(1.00)
20p loss 55 (21%) 202 0.00568
(1.00) 		0.0018
(0.954) 		0.00197
(1.00) 		0.0345
(1.00) 		0.671
(1.00) 		0.00377
(1.00) 		0.054
(1.00) 		0.0238
(1.00)
20q loss 25 (10%) 232 0.408
(1.00) 		0.125
(1.00) 		0.145
(1.00) 		0.674
(1.00) 		0.451
(1.00) 		0.17
(1.00) 		0.0973
(1.00) 		0.181
(1.00)
21q loss 50 (19%) 207 0.0425
(1.00) 		0.0592
(1.00) 		0.00535
(1.00) 		0.229
(1.00) 		0.114
(1.00) 		0.42
(1.00) 		0.329
(1.00) 		0.154
(1.00)
'1p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
1P GAIN MUTATED 7 5 11 2 2 22 3
1P GAIN WILD-TYPE 35 36 46 30 16 21 2

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.048

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
2P GAIN MUTATED 2 1 9 10
2P GAIN WILD-TYPE 66 75 54 36

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.18

Table S3.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
3P GAIN MUTATED 1 9 12 0 1 12 0
3P GAIN WILD-TYPE 41 32 45 32 17 31 5

Figure S3.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
3P GAIN MUTATED 4 13 22 0
3P GAIN WILD-TYPE 64 63 41 46

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.13

Table S5.  Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
3P GAIN MUTATED 3 4 9 0 19 4 0
3P GAIN WILD-TYPE 44 18 40 28 40 25 19

Figure S5.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.042

Table S6.  Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
3Q GAIN MUTATED 5 10 20 1
3Q GAIN WILD-TYPE 63 66 43 45

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.19

Table S7.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
4P GAIN MUTATED 14 8 11 4 2 23 2
4P GAIN WILD-TYPE 28 33 46 28 16 20 3

Figure S7.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S8.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
5P GAIN MUTATED 24 12 15 16 14 17 0
5P GAIN WILD-TYPE 2 46 28 35 20 27 1

Figure S8.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.06

Table S9.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
5P GAIN MUTATED 20 14 23 5 2 27 1
5P GAIN WILD-TYPE 22 27 34 27 16 16 4

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S10.  Gene #9: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
5P GAIN MUTATED 29 25 36 8
5P GAIN WILD-TYPE 39 51 27 38

Figure S10.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S11.  Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
5P GAIN MUTATED 26 4 21 6 33 4 4
5P GAIN WILD-TYPE 21 18 28 22 26 25 15

Figure S11.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S12.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
5Q GAIN MUTATED 17 8 9 13 14 10 0
5Q GAIN WILD-TYPE 9 50 34 38 20 34 1

Figure S12.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
6P GAIN MUTATED 20 6 5 4 0 12 1
6P GAIN WILD-TYPE 22 35 52 28 18 31 4

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

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.083

Table S14.  Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
6P GAIN MUTATED 21 3 3 3 15 3 3
6P GAIN WILD-TYPE 26 19 46 25 44 26 16

Figure S14.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S15.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
6Q GAIN MUTATED 11 4 16 3 6 10 0
6Q GAIN WILD-TYPE 15 54 27 48 28 34 1

Figure S15.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S16.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
6Q GAIN MUTATED 20 7 6 3 0 11 1
6Q GAIN WILD-TYPE 22 34 51 29 18 32 4

Figure S16.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.094

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
7Q GAIN MUTATED 20 11 24
7Q GAIN WILD-TYPE 65 53 21

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S18.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
9P GAIN MUTATED 9 2 11 6 14 15 0
9P GAIN WILD-TYPE 17 56 32 45 20 29 1

Figure S18.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S19.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
9Q GAIN MUTATED 13 4 16 8 16 16 0
9Q GAIN WILD-TYPE 13 54 27 43 18 28 1

Figure S19.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.25

Table S20.  Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
9Q GAIN MUTATED 19 10 11 5 0 18 1
9Q GAIN WILD-TYPE 23 31 46 27 18 25 4

Figure S20.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S21.  Gene #18: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
9Q GAIN MUTATED 23 9 10 6 23 2 0
9Q GAIN WILD-TYPE 24 13 39 22 36 27 19

Figure S21.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S22.  Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
12P GAIN MUTATED 8 4 18 13
12P GAIN WILD-TYPE 60 72 45 33

Figure S22.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.042

Table S23.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
15Q GAIN MUTATED 12 3 10 15 14 9 0
15Q GAIN WILD-TYPE 14 55 33 36 20 35 1

Figure S23.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S24.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
17P GAIN MUTATED 8 3 9 11 15 15 0
17P GAIN WILD-TYPE 18 55 34 40 19 29 1

Figure S24.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S25.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
17Q GAIN MUTATED 4 3 5 15 14 16 0
17Q GAIN WILD-TYPE 22 55 38 36 20 28 1

Figure S25.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S26.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
19P GAIN MUTATED 16 4 20 13 14 20 0
19P GAIN WILD-TYPE 10 54 23 38 20 24 1

Figure S26.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S27.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
19Q GAIN MUTATED 13 4 16 4 14 14 0
19Q GAIN WILD-TYPE 13 54 27 47 20 30 1

Figure S27.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.094

Table S28.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
19Q GAIN MUTATED 19 9 8 3 1 17 0
19Q GAIN WILD-TYPE 23 32 49 29 17 26 5

Figure S28.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S29.  Gene #35: '19q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
19Q GAIN MUTATED 24 4 6 8 19 4 0
19Q GAIN WILD-TYPE 23 18 43 20 40 25 19

Figure S29.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S30.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
20Q GAIN MUTATED 15 6 18 17 14 13 0
20Q GAIN WILD-TYPE 11 52 25 34 20 31 1

Figure S30.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.18

Table S31.  Gene #37: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
20Q GAIN MUTATED 22 16 34 11
20Q GAIN WILD-TYPE 46 60 29 35

Figure S31.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S32.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
21Q GAIN MUTATED 14 5 9 4 14 12 0
21Q GAIN WILD-TYPE 12 53 34 47 20 32 1

Figure S32.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.19

Table S33.  Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
22Q GAIN MUTATED 14 15 27 4
22Q GAIN WILD-TYPE 54 61 36 42

Figure S33.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S34.  Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
2P LOSS MUTATED 17 4 8 14 21 24 0
2P LOSS WILD-TYPE 9 54 35 37 13 20 1

Figure S34.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S35.  Gene #43: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
2P LOSS MUTATED 16 6 33 4 3 14 1
2P LOSS WILD-TYPE 26 35 24 28 15 29 4

Figure S35.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S36.  Gene #43: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
2P LOSS MUTATED 25 38 19 5
2P LOSS WILD-TYPE 43 38 44 41

Figure S36.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.089

Table S37.  Gene #43: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
2P LOSS MUTATED 21 6 28 4 17 10 1
2P LOSS WILD-TYPE 26 16 21 24 42 19 18

Figure S37.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S38.  Gene #43: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
2P LOSS MUTATED 25 7 55 1
2P LOSS WILD-TYPE 57 30 59 21

Figure S38.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S39.  Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
2Q LOSS MUTATED 16 5 7 8 14 21 0
2Q LOSS WILD-TYPE 10 53 36 43 20 23 1

Figure S39.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S40.  Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
3P LOSS MUTATED 20 4 3 7 1 11 2
3P LOSS WILD-TYPE 22 37 54 25 17 32 3

Figure S40.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S41.  Gene #45: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
3P LOSS MUTATED 23 5 13 15
3P LOSS WILD-TYPE 45 71 50 31

Figure S41.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.2

Table S42.  Gene #45: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
3P LOSS MUTATED 19 4 3 9 13 2 6
3P LOSS WILD-TYPE 28 18 46 19 46 27 13

Figure S42.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S43.  Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
10P LOSS MUTATED 12 9 15 38 22 24 0
10P LOSS WILD-TYPE 14 49 28 13 12 20 1

Figure S43.  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 = 0.0064

Table S44.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
10Q LOSS MUTATED 13 7 11 42 25 32 1
10Q LOSS WILD-TYPE 13 51 32 9 9 12 0

Figure S44.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S45.  Gene #60: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
10Q LOSS MUTATED 22 7 48 7 7 27 4
10Q LOSS WILD-TYPE 20 34 9 25 11 16 1

Figure S45.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S46.  Gene #60: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
10Q LOSS MUTATED 27 58 34 11
10Q LOSS WILD-TYPE 41 18 29 35

Figure S46.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S47.  Gene #60: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
10Q LOSS MUTATED 24 6 44 6 31 15 4
10Q LOSS WILD-TYPE 23 16 5 22 28 14 15

Figure S47.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S48.  Gene #60: '10q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
10Q LOSS MUTATED 38 25 68
10Q LOSS WILD-TYPE 71 22 31

Figure S48.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S49.  Gene #60: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
10Q LOSS MUTATED 35 14 79 3
10Q LOSS WILD-TYPE 47 23 35 19

Figure S49.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S50.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
10Q LOSS MUTATED 30 47 25
10Q LOSS WILD-TYPE 55 17 20

Figure S50.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S51.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
10Q LOSS MUTATED 12 12 31 13 8 11 10 5
10Q LOSS WILD-TYPE 12 20 6 10 4 12 11 17

Figure S51.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S52.  Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
11P LOSS MUTATED 10 3 25 16 16 24 0
11P LOSS WILD-TYPE 16 55 18 35 18 20 1

Figure S52.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.21

Table S53.  Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
11P LOSS MUTATED 25 7 23 9 2 16 3
11P LOSS WILD-TYPE 17 34 34 23 16 27 2

Figure S53.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S54.  Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
11Q LOSS MUTATED 9 4 25 11 13 29 0
11Q LOSS WILD-TYPE 17 54 18 40 21 15 1

Figure S54.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.18

Table S55.  Gene #62: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
11Q LOSS MUTATED 25 8 19 9 1 16 3
11Q LOSS WILD-TYPE 17 33 38 23 17 27 2

Figure S55.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S56.  Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
12P LOSS MUTATED 14 5 9 6 14 16 1
12P LOSS WILD-TYPE 12 53 34 45 20 28 0

Figure S56.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S57.  Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
13Q LOSS MUTATED 16 13 22 36 24 21 0
13Q LOSS WILD-TYPE 10 45 21 15 10 23 1

Figure S57.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S58.  Gene #65: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
13Q LOSS MUTATED 29 40 46 15
13Q LOSS WILD-TYPE 39 36 17 31

Figure S58.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S59.  Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
14Q LOSS MUTATED 4 4 15 15 2 21 0
14Q LOSS WILD-TYPE 22 54 28 36 32 23 1

Figure S59.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S60.  Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
16Q LOSS MUTATED 14 10 19 31 24 25 1
16Q LOSS WILD-TYPE 12 48 24 20 10 19 0

Figure S60.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.089

Table S61.  Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
16Q LOSS MUTATED 23 10 40 10 8 25 2
16Q LOSS WILD-TYPE 19 31 17 22 10 18 3

Figure S61.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.13

Table S62.  Gene #69: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
16Q LOSS MUTATED 39 9 69 6
16Q LOSS WILD-TYPE 43 28 45 16

Figure S62.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.089

Table S63.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
16Q LOSS MUTATED 30 44 25
16Q LOSS WILD-TYPE 55 20 20

Figure S63.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S64.  Gene #74: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
19P LOSS MUTATED 1 4 14 2
19P LOSS WILD-TYPE 67 72 49 44

Figure S64.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.042

Table S65.  Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
22Q LOSS MUTATED 8 5 8 10 15 19 1
22Q LOSS WILD-TYPE 18 53 35 41 19 25 0

Figure S65.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S66.  Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
XQ LOSS MUTATED 7 5 17 21 18 26 1
XQ LOSS WILD-TYPE 19 53 26 30 16 18 0

Figure S66.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S67.  Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
XQ LOSS MUTATED 17 3 34 8 9 15 1
XQ LOSS WILD-TYPE 25 38 23 24 9 28 4

Figure S67.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S68.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
XQ LOSS MUTATED 25 44 14 11
XQ LOSS WILD-TYPE 43 32 49 35

Figure S68.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.15

Table S69.  Gene #80: 'xq loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
XQ LOSS MUTATED 19 3 28 11 13 16 4
XQ LOSS WILD-TYPE 28 19 21 17 46 13 15

Figure S69.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 257

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 8

  • 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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