Correlation between copy number variations of arm-level result and molecular subtypes
Sarcoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C170806Z
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/C170806Z
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 169 patients, 42 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'.

  • 4p gain cnv correlated to 'METHLYATION_CNMF'.

  • 5p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

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

  • 20q gain cnv correlated to 'CN_CNMF'.

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

  • 2q loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'METHLYATION_CNMF'.

  • 3q loss cnv correlated to 'METHLYATION_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'.

  • 13q loss cnv correlated to 'METHLYATION_CNMF'.

  • 16p loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF'.

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

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, 42 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 91 (54%) 78 1e-05
(0.0064) 		1e-05
(0.0064) 		1e-05
(0.0064) 		1e-05
(0.0064) 		3e-05
(0.0188) 		2e-05
(0.0126) 		1e-05
(0.0064) 		7e-05
(0.0434)
6p gain 37 (22%) 132 3e-05
(0.0188) 		2e-05
(0.0126) 		3e-05
(0.0188) 		1e-05
(0.0064) 		0.00778
(1.00) 		3e-05
(0.0188) 		0.00159
(0.914) 		0.0104
(1.00)
6q gain 35 (21%) 134 0.00041
(0.246) 		0.00025
(0.151) 		0.00011
(0.0678) 		0.00042
(0.251) 		0.00724
(1.00) 		0.00124
(0.722) 		0.00155
(0.893) 		0.00903
(1.00)
19q gain 39 (23%) 130 2e-05
(0.0126) 		0.00019
(0.116) 		0.00031
(0.186) 		0.0006
(0.356) 		0.147
(1.00) 		0.00059
(0.351) 		0.0302
(1.00) 		0.136
(1.00)
2p loss 50 (30%) 119 0.0001
(0.0617) 		7e-05
(0.0434) 		0.0015
(0.867) 		5e-05
(0.0311) 		0.00976
(1.00) 		0.00468
(1.00) 		0.00289
(1.00) 		0.00232
(1.00)
11p loss 62 (37%) 107 6e-05
(0.0373) 		9e-05
(0.0556) 		0.5
(1.00) 		0.699
(1.00) 		0.463
(1.00) 		0.584
(1.00) 		0.6
(1.00) 		0.304
(1.00)
xq loss 62 (37%) 107 0.00797
(1.00) 		5e-05
(0.0311) 		0.00114
(0.666) 		0.0023
(1.00) 		0.0017
(0.976) 		0.00181
(1.00) 		0.00018
(0.11) 		0.00066
(0.391)
1p gain 38 (22%) 131 0.00282
(1.00) 		0.00023
(0.14) 		0.0295
(1.00) 		0.0776
(1.00) 		0.121
(1.00) 		0.332
(1.00) 		0.228
(1.00) 		0.203
(1.00)
2p gain 16 (9%) 153 0.00112
(0.655) 		0.017
(1.00) 		0.00021
(0.128) 		0.0144
(1.00) 		0.00705
(1.00) 		0.0207
(1.00) 		0.00426
(1.00) 		0.0173
(1.00)
4p gain 43 (25%) 126 0.00134
(0.777) 		0.00027
(0.163) 		0.00152
(0.877) 		0.00065
(0.385) 		0.00426
(1.00) 		0.00861
(1.00) 		0.0248
(1.00) 		0.0327
(1.00)
5p gain 55 (33%) 114 0.00215
(1.00) 		0.00838
(1.00) 		0.0659
(1.00) 		0.00012
(0.0738) 		0.49
(1.00) 		0.0314
(1.00) 		0.393
(1.00) 		0.4
(1.00)
9q gain 42 (25%) 127 0.00013
(0.0798) 		0.00866
(1.00) 		0.0108
(1.00) 		0.0171
(1.00) 		0.0574
(1.00) 		0.0191
(1.00) 		0.00518
(1.00) 		0.0683
(1.00)
17p gain 39 (23%) 130 0.00018
(0.11) 		0.006
(1.00) 		0.00687
(1.00) 		0.0236
(1.00) 		0.0542
(1.00) 		0.00605
(1.00) 		0.0937
(1.00) 		0.0246
(1.00)
18p gain 26 (15%) 143 0.00027
(0.163) 		0.0505
(1.00) 		0.657
(1.00) 		0.486
(1.00) 		0.491
(1.00) 		0.197
(1.00) 		1
(1.00) 		0.551
(1.00)
19p gain 54 (32%) 115 1e-05
(0.0064) 		0.0164
(1.00) 		0.0624
(1.00) 		0.0415
(1.00) 		0.747
(1.00) 		0.325
(1.00) 		0.464
(1.00) 		0.319
(1.00)
20q gain 58 (34%) 111 0.00025
(0.151) 		0.053
(1.00) 		0.00724
(1.00) 		0.0283
(1.00) 		0.257
(1.00) 		0.00671
(1.00) 		0.18
(1.00) 		0.0834
(1.00)
2q loss 45 (27%) 124 0.00029
(0.175) 		0.0442
(1.00) 		0.486
(1.00) 		0.346
(1.00) 		0.971
(1.00) 		0.944
(1.00) 		0.798
(1.00) 		0.724
(1.00)
3p loss 34 (20%) 135 0.0213
(1.00) 		1e-05
(0.0064) 		0.00268
(1.00) 		0.0216
(1.00) 		0.00401
(1.00) 		0.0077
(1.00) 		0.00078
(0.459) 		0.00884
(1.00)
3q loss 38 (22%) 131 0.00515
(1.00) 		0.00037
(0.222) 		0.015
(1.00) 		0.112
(1.00) 		0.0325
(1.00) 		0.023
(1.00) 		0.00921
(1.00) 		0.0247
(1.00)
11q loss 56 (33%) 113 1e-05
(0.0064) 		0.00248
(1.00) 		0.335
(1.00) 		0.395
(1.00) 		0.254
(1.00) 		0.238
(1.00) 		0.256
(1.00) 		0.305
(1.00)
13q loss 88 (52%) 81 0.00278
(1.00) 		0.00013
(0.0798) 		0.0105
(1.00) 		0.0105
(1.00) 		0.613
(1.00) 		0.308
(1.00) 		0.414
(1.00) 		0.299
(1.00)
16p loss 48 (28%) 121 0.00014
(0.0857) 		0.0266
(1.00) 		0.316
(1.00) 		0.335
(1.00) 		0.706
(1.00) 		0.741
(1.00) 		1
(1.00) 		0.505
(1.00)
16q loss 86 (51%) 83 1e-05
(0.0064) 		0.00055
(0.328) 		0.00294
(1.00) 		0.00336
(1.00) 		0.00741
(1.00) 		0.0116
(1.00) 		0.001
(0.586) 		0.0215
(1.00)
1q gain 37 (22%) 132 0.00696
(1.00) 		0.0384
(1.00) 		0.0918
(1.00) 		0.157
(1.00) 		0.902
(1.00) 		0.776
(1.00) 		0.645
(1.00) 		0.64
(1.00)
2q gain 12 (7%) 157 0.00142
(0.822) 		0.273
(1.00) 		0.0173
(1.00) 		0.231
(1.00) 		0.0749
(1.00) 		0.135
(1.00) 		0.0469
(1.00) 		0.103
(1.00)
3p gain 20 (12%) 149 0.032
(1.00) 		0.00471
(1.00) 		0.00066
(0.391) 		0.00273
(1.00) 		0.899
(1.00) 		0.82
(1.00) 		0.773
(1.00) 		0.707
(1.00)
3q gain 19 (11%) 150 0.0486
(1.00) 		0.0257
(1.00) 		0.00171
(0.98) 		0.0262
(1.00) 		0.946
(1.00) 		0.746
(1.00) 		0.762
(1.00) 		0.734
(1.00)
4q gain 32 (19%) 137 0.142
(1.00) 		0.0121
(1.00) 		0.0361
(1.00) 		0.0128
(1.00) 		0.094
(1.00) 		0.0784
(1.00) 		0.1
(1.00) 		0.338
(1.00)
5q gain 44 (26%) 125 0.0569
(1.00) 		0.113
(1.00) 		0.628
(1.00) 		0.0619
(1.00) 		0.19
(1.00) 		0.116
(1.00) 		0.172
(1.00) 		0.662
(1.00)
7p gain 53 (31%) 116 0.00073
(0.431) 		0.0605
(1.00) 		0.216
(1.00) 		0.559
(1.00) 		0.399
(1.00) 		0.38
(1.00) 		0.084
(1.00) 		0.36
(1.00)
7q gain 42 (25%) 127 0.00424
(1.00) 		0.0338
(1.00) 		0.275
(1.00) 		0.245
(1.00) 		0.228
(1.00) 		0.232
(1.00) 		0.106
(1.00) 		0.0924
(1.00)
8p gain 38 (22%) 131 0.0531
(1.00) 		0.758
(1.00) 		0.768
(1.00) 		0.321
(1.00) 		0.626
(1.00) 		0.137
(1.00) 		0.375
(1.00) 		0.617
(1.00)
8q gain 46 (27%) 123 0.0245
(1.00) 		0.0204
(1.00) 		0.0349
(1.00) 		0.341
(1.00) 		0.606
(1.00) 		0.065
(1.00) 		0.393
(1.00) 		0.473
(1.00)
9p gain 33 (20%) 136 0.00129
(0.749) 		0.011
(1.00) 		0.0234
(1.00) 		0.0712
(1.00) 		0.0431
(1.00) 		0.0866
(1.00) 		0.0553
(1.00) 		0.119
(1.00)
10p gain 14 (8%) 155 0.0243
(1.00) 		0.0235
(1.00) 		0.152
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.5
(1.00) 		0.807
(1.00)
10q gain 5 (3%) 164 0.32
(1.00) 		0.52
(1.00) 		0.101
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.0187
(1.00) 		0.482
(1.00) 		0.611
(1.00)
11p gain 14 (8%) 155 0.084
(1.00) 		0.0499
(1.00) 		0.136
(1.00) 		0.0919
(1.00) 		1
(1.00) 		0.233
(1.00) 		0.334
(1.00) 		1
(1.00)
11q gain 12 (7%) 157 0.387
(1.00) 		0.145
(1.00) 		0.343
(1.00) 		0.101
(1.00) 		0.459
(1.00) 		0.589
(1.00) 		0.34
(1.00) 		0.686
(1.00)
12p gain 25 (15%) 144 0.109
(1.00) 		0.125
(1.00) 		0.0188
(1.00) 		0.103
(1.00) 		0.618
(1.00) 		0.00611
(1.00) 		0.353
(1.00) 		0.0835
(1.00)
12q gain 18 (11%) 151 0.151
(1.00) 		0.224
(1.00) 		0.247
(1.00) 		0.608
(1.00) 		0.78
(1.00) 		0.0264
(1.00) 		0.404
(1.00) 		0.562
(1.00)
13q gain 8 (5%) 161 0.154
(1.00) 		0.187
(1.00) 		0.185
(1.00) 		0.121
(1.00) 		0.673
(1.00) 		0.472
(1.00) 		0.379
(1.00) 		0.319
(1.00)
14q gain 37 (22%) 132 0.423
(1.00) 		0.147
(1.00) 		0.227
(1.00) 		0.285
(1.00) 		0.382
(1.00) 		0.627
(1.00) 		0.401
(1.00) 		0.254
(1.00)
15q gain 42 (25%) 127 0.0258
(1.00) 		0.102
(1.00) 		0.503
(1.00) 		0.316
(1.00) 		0.263
(1.00) 		0.425
(1.00) 		0.362
(1.00) 		0.35
(1.00)
16p gain 25 (15%) 144 0.0332
(1.00) 		0.037
(1.00) 		0.658
(1.00) 		0.264
(1.00) 		0.697
(1.00) 		0.281
(1.00) 		0.572
(1.00) 		0.608
(1.00)
16q gain 11 (7%) 158 0.163
(1.00) 		0.106
(1.00) 		0.149
(1.00) 		0.419
(1.00) 		0.0375
(1.00) 		0.0741
(1.00) 		0.0454
(1.00) 		0.551
(1.00)
17q gain 33 (20%) 136 0.0067
(1.00) 		0.0413
(1.00) 		0.0403
(1.00) 		0.00368
(1.00) 		0.101
(1.00) 		0.0581
(1.00) 		0.196
(1.00) 		0.0481
(1.00)
18q gain 21 (12%) 148 0.0958
(1.00) 		0.0662
(1.00) 		0.297
(1.00) 		0.915
(1.00) 		0.619
(1.00) 		0.959
(1.00) 		0.863
(1.00) 		0.75
(1.00)
20p gain 45 (27%) 124 0.0106
(1.00) 		0.244
(1.00) 		0.679
(1.00) 		0.66
(1.00) 		0.62
(1.00) 		0.384
(1.00) 		0.192
(1.00) 		0.827
(1.00)
21q gain 42 (25%) 127 0.00076
(0.448) 		0.0103
(1.00) 		0.184
(1.00) 		0.21
(1.00) 		0.564
(1.00) 		0.0332
(1.00) 		0.638
(1.00) 		0.551
(1.00)
22q gain 44 (26%) 125 0.0184
(1.00) 		0.158
(1.00) 		0.0622
(1.00) 		0.156
(1.00) 		0.759
(1.00) 		0.387
(1.00) 		0.887
(1.00) 		0.384
(1.00)
xq gain 22 (13%) 147 0.0735
(1.00) 		0.132
(1.00) 		0.208
(1.00) 		0.564
(1.00) 		0.219
(1.00) 		0.411
(1.00) 		0.316
(1.00) 		0.191
(1.00)
1p loss 23 (14%) 146 0.748
(1.00) 		0.17
(1.00) 		0.712
(1.00) 		0.242
(1.00) 		0.906
(1.00) 		0.442
(1.00) 		0.869
(1.00) 		0.957
(1.00)
1q loss 23 (14%) 146 0.0513
(1.00) 		0.067
(1.00) 		0.976
(1.00) 		0.905
(1.00) 		0.644
(1.00) 		0.449
(1.00) 		0.546
(1.00) 		0.648
(1.00)
4p loss 25 (15%) 144 0.159
(1.00) 		0.133
(1.00) 		0.0896
(1.00) 		0.512
(1.00) 		0.3
(1.00) 		0.647
(1.00) 		0.18
(1.00) 		0.54
(1.00)
4q loss 29 (17%) 140 0.019
(1.00) 		0.00425
(1.00) 		0.0778
(1.00) 		0.363
(1.00) 		0.884
(1.00) 		0.767
(1.00) 		0.79
(1.00) 		0.663
(1.00)
5p loss 19 (11%) 150 0.822
(1.00) 		0.00262
(1.00) 		0.0223
(1.00) 		0.0189
(1.00) 		0.129
(1.00) 		0.0689
(1.00) 		0.0422
(1.00) 		0.136
(1.00)
5q loss 27 (16%) 142 0.122
(1.00) 		0.0892
(1.00) 		0.042
(1.00) 		0.0917
(1.00) 		0.407
(1.00) 		0.138
(1.00) 		0.188
(1.00) 		0.3
(1.00)
6p loss 43 (25%) 126 0.753
(1.00) 		0.202
(1.00) 		0.0693
(1.00) 		0.0719
(1.00) 		0.337
(1.00) 		0.298
(1.00) 		0.336
(1.00) 		0.345
(1.00)
6q loss 31 (18%) 138 0.0424
(1.00) 		0.0213
(1.00) 		0.0909
(1.00) 		0.0868
(1.00) 		0.158
(1.00) 		0.922
(1.00) 		0.285
(1.00) 		0.787
(1.00)
7p loss 23 (14%) 146 0.0727
(1.00) 		0.00632
(1.00) 		0.138
(1.00) 		0.0543
(1.00) 		0.907
(1.00) 		0.3
(1.00) 		0.518
(1.00) 		0.918
(1.00)
7q loss 22 (13%) 147 0.44
(1.00) 		0.433
(1.00) 		0.535
(1.00) 		0.292
(1.00) 		0.779
(1.00) 		0.948
(1.00) 		1
(1.00) 		0.797
(1.00)
8p loss 38 (22%) 131 0.234
(1.00) 		0.00096
(0.564) 		0.108
(1.00) 		0.085
(1.00) 		0.0463
(1.00) 		0.18
(1.00) 		0.122
(1.00) 		0.0408
(1.00)
8q loss 24 (14%) 145 0.0294
(1.00) 		0.0181
(1.00) 		0.0727
(1.00) 		0.173
(1.00) 		0.03
(1.00) 		0.06
(1.00) 		0.0324
(1.00) 		0.0867
(1.00)
9p loss 55 (33%) 114 0.0269
(1.00) 		0.108
(1.00) 		0.0656
(1.00) 		0.0517
(1.00) 		0.764
(1.00) 		0.169
(1.00) 		0.349
(1.00) 		0.327
(1.00)
9q loss 36 (21%) 133 0.239
(1.00) 		0.0489
(1.00) 		0.0336
(1.00) 		0.168
(1.00) 		0.783
(1.00) 		0.0702
(1.00) 		0.875
(1.00) 		0.704
(1.00)
10p loss 80 (47%) 89 0.00708
(1.00) 		0.00808
(1.00) 		0.0106
(1.00) 		0.00119
(0.694) 		0.0414
(1.00) 		0.104
(1.00) 		0.0349
(1.00) 		0.0413
(1.00)
12p loss 45 (27%) 124 0.0022
(1.00) 		0.00542
(1.00) 		0.548
(1.00) 		0.0863
(1.00) 		0.722
(1.00) 		0.557
(1.00) 		0.507
(1.00) 		0.34
(1.00)
12q loss 38 (22%) 131 0.00174
(0.995) 		0.0994
(1.00) 		0.91
(1.00) 		0.435
(1.00) 		0.716
(1.00) 		0.891
(1.00) 		0.683
(1.00) 		0.72
(1.00)
14q loss 47 (28%) 122 0.662
(1.00) 		0.0161
(1.00) 		0.781
(1.00) 		0.00464
(1.00) 		0.419
(1.00) 		0.179
(1.00) 		0.146
(1.00) 		0.211
(1.00)
15q loss 27 (16%) 142 0.0603
(1.00) 		0.103
(1.00) 		0.043
(1.00) 		0.0216
(1.00) 		0.132
(1.00) 		0.176
(1.00) 		0.144
(1.00) 		0.109
(1.00)
17p loss 34 (20%) 135 0.652
(1.00) 		0.19
(1.00) 		0.0366
(1.00) 		0.28
(1.00) 		0.597
(1.00) 		0.256
(1.00) 		0.495
(1.00) 		0.124
(1.00)
17q loss 33 (20%) 136 0.145
(1.00) 		0.0547
(1.00) 		0.124
(1.00) 		0.105
(1.00) 		0.712
(1.00) 		0.886
(1.00) 		0.839
(1.00) 		0.442
(1.00)
18p loss 42 (25%) 127 0.118
(1.00) 		0.333
(1.00) 		0.415
(1.00) 		0.934
(1.00) 		0.91
(1.00) 		0.976
(1.00) 		1
(1.00) 		0.842
(1.00)
18q loss 44 (26%) 125 0.0178
(1.00) 		0.101
(1.00) 		0.115
(1.00) 		0.316
(1.00) 		0.889
(1.00) 		0.666
(1.00) 		0.819
(1.00) 		0.923
(1.00)
19p loss 13 (8%) 156 0.0504
(1.00) 		0.00187
(1.00) 		0.00057
(0.34) 		0.0348
(1.00) 		1
(1.00) 		0.493
(1.00) 		0.79
(1.00) 		0.537
(1.00)
19q loss 28 (17%) 141 0.0351
(1.00) 		0.109
(1.00) 		0.0218
(1.00) 		0.22
(1.00) 		0.27
(1.00) 		0.921
(1.00) 		0.439
(1.00) 		0.514
(1.00)
20p loss 29 (17%) 140 0.321
(1.00) 		0.064
(1.00) 		0.168
(1.00) 		0.461
(1.00) 		0.96
(1.00) 		0.448
(1.00) 		0.926
(1.00) 		0.37
(1.00)
20q loss 10 (6%) 159 0.151
(1.00) 		0.324
(1.00) 		0.339
(1.00) 		1
(1.00) 		0.321
(1.00) 		0.492
(1.00) 		0.677
(1.00) 		0.64
(1.00)
21q loss 31 (18%) 138 0.0169
(1.00) 		0.163
(1.00) 		0.188
(1.00) 		0.148
(1.00) 		0.0753
(1.00) 		0.511
(1.00) 		0.31
(1.00) 		0.391
(1.00)
22q loss 45 (27%) 124 0.00429
(1.00) 		0.15
(1.00) 		0.932
(1.00) 		0.195
(1.00) 		0.718
(1.00) 		0.6
(1.00) 		0.712
(1.00) 		0.106
(1.00)
'1p gain' versus 'METHLYATION_CNMF'

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

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 30 28 42 21 16 28 4
1P GAIN MUTATED 6 4 7 2 1 15 3
1P GAIN WILD-TYPE 24 24 35 19 15 13 1

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

'2p gain' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 45 24 58
2P GAIN MUTATED 5 2 8 1
2P GAIN WILD-TYPE 34 43 16 57

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

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.16

Table S3.  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 30 28 42 21 16 28 4
4P GAIN MUTATED 11 6 6 2 1 16 1
4P GAIN WILD-TYPE 19 22 36 19 15 12 3

Figure S3.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.074

Table S4.  Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 32 33 37 19
5P GAIN MUTATED 20 5 15 15 0
5P GAIN WILD-TYPE 25 27 18 22 19

Figure S4.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S5.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
6P GAIN MUTATED 9 25 3
6P GAIN WILD-TYPE 37 41 54

Figure S5.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S6.  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 30 28 42 21 16 28 4
6P GAIN MUTATED 16 6 2 4 0 8 1
6P GAIN WILD-TYPE 14 22 40 17 16 20 3

Figure S6.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S7.  Gene #11: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 45 24 58
6P GAIN MUTATED 10 20 4 3
6P GAIN WILD-TYPE 29 25 20 55

Figure S7.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S8.  Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 32 33 37 19
6P GAIN MUTATED 21 4 9 1 2
6P GAIN WILD-TYPE 24 28 24 36 17

Figure S8.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S9.  Gene #11: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 14 29 12 60
6P GAIN MUTATED 16 6 10 2 2
6P GAIN WILD-TYPE 36 8 19 10 58

Figure S9.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

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

Table S10.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
6Q GAIN MUTATED 11 21 3
6Q GAIN WILD-TYPE 35 45 54

Figure S10.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.15

Table S11.  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 30 28 42 21 16 28 4
6Q GAIN MUTATED 15 6 3 3 0 7 1
6Q GAIN WILD-TYPE 15 22 39 18 16 21 3

Figure S11.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.068

Table S12.  Gene #12: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 45 24 58
6Q GAIN MUTATED 9 19 3 4
6Q GAIN WILD-TYPE 30 26 21 54

Figure S12.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.08

Table S13.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
9Q GAIN MUTATED 10 27 5
9Q GAIN WILD-TYPE 36 39 52

Figure S13.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

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

Table S14.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
17P GAIN MUTATED 8 26 5
17P GAIN WILD-TYPE 38 40 52

Figure S14.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.16

Table S15.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
18P GAIN MUTATED 5 19 2
18P GAIN WILD-TYPE 41 47 55

Figure S15.  Get High-res Image Gene #32: '18p 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 S16.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
19P GAIN MUTATED 13 37 4
19P GAIN WILD-TYPE 33 29 53

Figure S16.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S17.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
19Q GAIN MUTATED 8 27 4
19Q GAIN WILD-TYPE 38 39 53

Figure S17.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

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

Table S18.  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 30 28 42 21 16 28 4
19Q GAIN MUTATED 15 6 4 2 1 11 0
19Q GAIN WILD-TYPE 15 22 38 19 15 17 4

Figure S18.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

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

Table S19.  Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 45 24 58
19Q GAIN MUTATED 13 18 3 5
19Q GAIN WILD-TYPE 26 27 21 53

Figure S19.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.15

Table S20.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
20Q GAIN MUTATED 14 34 10
20Q GAIN WILD-TYPE 32 32 47

Figure S20.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.062

Table S21.  Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
2P LOSS MUTATED 7 32 11
2P LOSS WILD-TYPE 39 34 46

Figure S21.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.043

Table S22.  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 30 28 42 21 16 28 4
2P LOSS MUTATED 10 3 24 2 2 9 0
2P LOSS WILD-TYPE 20 25 18 19 14 19 4

Figure S22.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.031

Table S23.  Gene #43: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 32 33 37 19
2P LOSS MUTATED 14 1 8 21 5
2P LOSS WILD-TYPE 31 31 25 16 14

Figure S23.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.17

Table S24.  Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
2Q LOSS MUTATED 8 29 8
2Q LOSS WILD-TYPE 38 37 49

Figure S24.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

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

Table S25.  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 30 28 42 21 16 28 4
3P LOSS MUTATED 16 2 2 4 1 8 1
3P LOSS WILD-TYPE 14 26 40 17 15 20 3

Figure S25.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.22

Table S26.  Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 42 21 16 28 4
3Q LOSS MUTATED 15 3 4 4 1 10 1
3Q LOSS WILD-TYPE 15 25 38 17 15 18 3

Figure S26.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'CN_CNMF'

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

Table S27.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
10Q LOSS MUTATED 8 50 33
10Q LOSS WILD-TYPE 38 16 24

Figure S27.  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 S28.  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 30 28 42 21 16 28 4
10Q LOSS MUTATED 14 4 37 5 7 20 4
10Q LOSS WILD-TYPE 16 24 5 16 9 8 0

Figure S28.  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 S29.  Gene #60: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 45 24 58
10Q LOSS MUTATED 22 13 7 47
10Q LOSS WILD-TYPE 17 32 17 11

Figure S29.  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 S30.  Gene #60: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 32 33 37 19
10Q LOSS MUTATED 15 9 19 34 12
10Q LOSS WILD-TYPE 30 23 14 3 7

Figure S30.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S31.  Gene #60: '10q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 71 23
10Q LOSS MUTATED 26 52 12
10Q LOSS WILD-TYPE 47 19 11

Figure S31.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S32.  Gene #60: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 14 29 12 60
10Q LOSS MUTATED 21 7 13 2 47
10Q LOSS WILD-TYPE 31 7 16 10 13

Figure S32.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S33.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 71 27
10Q LOSS MUTATED 23 53 14
10Q LOSS WILD-TYPE 46 18 13

Figure S33.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.043

Table S34.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 72 33
10Q LOSS MUTATED 21 52 17
10Q LOSS WILD-TYPE 41 20 16

Figure S34.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S35.  Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
11P LOSS MUTATED 23 31 8
11P LOSS WILD-TYPE 23 35 49

Figure S35.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.056

Table S36.  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 30 28 42 21 16 28 4
11P LOSS MUTATED 21 4 16 7 1 11 2
11P LOSS WILD-TYPE 9 24 26 14 15 17 2

Figure S36.  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 S37.  Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
11Q LOSS MUTATED 21 30 5
11Q LOSS WILD-TYPE 25 36 52

Figure S37.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.08

Table S38.  Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 42 21 16 28 4
13Q LOSS MUTATED 21 11 21 8 4 23 0
13Q LOSS WILD-TYPE 9 17 21 13 12 5 4

Figure S38.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.086

Table S39.  Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
16P LOSS MUTATED 6 31 11
16P LOSS WILD-TYPE 40 35 46

Figure S39.  Get High-res Image Gene #68: '16p 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 S40.  Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 66 57
16Q LOSS MUTATED 11 47 28
16Q LOSS WILD-TYPE 35 19 29

Figure S40.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.031

Table S41.  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 30 28 42 21 16 28 4
XQ LOSS MUTATED 9 1 25 7 8 12 0
XQ LOSS WILD-TYPE 21 27 17 14 8 16 4

Figure S41.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S42.  Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 71 27
XQ LOSS MUTATED 15 39 7
XQ LOSS WILD-TYPE 54 32 20

Figure S42.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 169

  • 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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