Correlation between copy number variations of arm-level result and molecular subtypes
Sarcoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C13T9F93
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13T9F93
Overview
Introduction

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

Summary

Testing the association between copy number variation 65 arm-level results and 6 molecular subtypes across 52 patients, no significant finding detected with Q value < 0.25.

  • No arm-level cnvs related to molecular subtypes.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 65 arm-level results and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		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
1p gain 0 (0%) 44 0.233
(1.00) 		0.243
(1.00) 		0.573
(1.00) 		0.606
(1.00) 		0.573
(1.00) 		0.606
(1.00)
1q gain 0 (0%) 45 0.392
(1.00) 		0.00716
(1.00) 		0.0783
(1.00) 		0.164
(1.00) 		0.0783
(1.00) 		0.164
(1.00)
2p gain 0 (0%) 49 0.326
(1.00) 		0.0992
(1.00) 		1
(1.00) 		1
(1.00)
4p gain 0 (0%) 47 0.522
(1.00) 		0.602
(1.00)
5p gain 0 (0%) 39 0.0243
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
5q gain 0 (0%) 41 0.0212
(1.00) 		0.334
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
6p gain 0 (0%) 44 0.207
(1.00) 		0.075
(1.00) 		0.107
(1.00) 		0.235
(1.00) 		0.107
(1.00) 		0.235
(1.00)
6q gain 0 (0%) 42 0.0084
(1.00) 		0.0219
(1.00) 		0.0476
(1.00) 		0.0926
(1.00) 		0.0476
(1.00) 		0.0926
(1.00)
7p gain 0 (0%) 39 0.022
(1.00) 		0.268
(1.00) 		0.632
(1.00) 		0.283
(1.00) 		0.632
(1.00) 		0.283
(1.00)
7q gain 0 (0%) 41 0.127
(1.00) 		0.116
(1.00) 		0.632
(1.00) 		0.283
(1.00) 		0.632
(1.00) 		0.283
(1.00)
8p gain 0 (0%) 43 0.0657
(1.00) 		0.899
(1.00) 		0.632
(1.00) 		0.689
(1.00) 		0.632
(1.00) 		0.689
(1.00)
8q gain 0 (0%) 44 0.138
(1.00) 		0.106
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
9p gain 0 (0%) 48 0.0316
(1.00) 		0.444
(1.00) 		0.488
(1.00) 		0.488
(1.00)
9q gain 0 (0%) 45 0.0122
(1.00) 		0.363
(1.00) 		0.107
(1.00) 		0.235
(1.00) 		0.107
(1.00) 		0.235
(1.00)
12p gain 0 (0%) 45 0.58
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
14q gain 0 (0%) 49 1
(1.00) 		0.765
(1.00) 		1
(1.00) 		1
(1.00)
15q gain 0 (0%) 44 0.264
(1.00) 		0.708
(1.00) 		1
(1.00) 		1
(1.00)
16p gain 0 (0%) 45 0.672
(1.00) 		0.19
(1.00) 		0.573
(1.00) 		0.606
(1.00) 		0.573
(1.00) 		0.606
(1.00)
17p gain 0 (0%) 44 0.0102
(1.00) 		0.00203
(0.712) 		1
(1.00) 		1
(1.00)
17q gain 0 (0%) 46 0.301
(1.00) 		0.341
(1.00) 		0.573
(1.00) 		0.103
(1.00) 		0.573
(1.00) 		0.103
(1.00)
18p gain 0 (0%) 45 1
(1.00) 		0.475
(1.00) 		1
(1.00) 		1
(1.00)
18q gain 0 (0%) 44 0.138
(1.00) 		0.708
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
19p gain 0 (0%) 42 0.0096
(1.00) 		0.568
(1.00) 		0.573
(1.00) 		0.103
(1.00) 		0.573
(1.00) 		0.103
(1.00)
19q gain 0 (0%) 46 0.0217
(1.00) 		0.666
(1.00)
20p gain 0 (0%) 39 0.423
(1.00) 		0.229
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
20q gain 0 (0%) 36 0.0728
(1.00) 		0.0266
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
21q gain 0 (0%) 45 0.772
(1.00) 		0.152
(1.00) 		1
(1.00) 		1
(1.00)
22q gain 0 (0%) 47 0.344
(1.00) 		0.856
(1.00) 		0.448
(1.00) 		0.448
(1.00)
1p loss 0 (0%) 43 0.168
(1.00) 		0.343
(1.00) 		0.144
(1.00) 		0.0558
(1.00) 		0.144
(1.00) 		0.0558
(1.00)
1q loss 0 (0%) 46 0.481
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 0 (0%) 42 1
(1.00) 		0.3
(1.00) 		0.632
(1.00) 		0.689
(1.00) 		0.632
(1.00) 		0.689
(1.00)
2q loss 0 (0%) 44 0.623
(1.00) 		0.502
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
3p loss 0 (0%) 42 0.0902
(1.00) 		0.676
(1.00) 		0.107
(1.00) 		0.235
(1.00) 		0.107
(1.00) 		0.235
(1.00)
3q loss 0 (0%) 39 0.0163
(1.00) 		0.314
(1.00) 		0.183
(1.00) 		0.363
(1.00) 		0.183
(1.00) 		0.363
(1.00)
4p loss 0 (0%) 46 0.21
(1.00) 		0.255
(1.00) 		0.488
(1.00) 		0.488
(1.00)
4q loss 0 (0%) 46 0.415
(1.00) 		0.255
(1.00) 		0.488
(1.00) 		0.488
(1.00)
5p loss 0 (0%) 48 0.112
(1.00) 		1
(1.00) 		0.488
(1.00) 		0.488
(1.00)
5q loss 0 (0%) 47 0.522
(1.00) 		0.351
(1.00) 		0.488
(1.00) 		0.488
(1.00)
6p loss 0 (0%) 44 0.794
(1.00) 		0.243
(1.00) 		0.364
(1.00) 		0.488
(1.00) 		0.364
(1.00) 		0.488
(1.00)
6q loss 0 (0%) 48 0.664
(1.00) 		0.309
(1.00) 		1
(1.00) 		1
(1.00)
7p loss 0 (0%) 48 0.341
(1.00) 		0.309
(1.00) 		0.573
(1.00) 		0.606
(1.00) 		0.573
(1.00) 		0.606
(1.00)
7q loss 0 (0%) 46 0.301
(1.00) 		0.255
(1.00) 		0.606
(1.00) 		0.667
(1.00) 		0.606
(1.00) 		0.667
(1.00)
8p loss 0 (0%) 42 0.324
(1.00) 		0.369
(1.00) 		0.663
(1.00) 		0.119
(1.00) 		0.663
(1.00) 		0.119
(1.00)
8q loss 0 (0%) 47 0.718
(1.00) 		0.0335
(1.00) 		0.232
(1.00) 		0.317
(1.00) 		0.232
(1.00) 		0.317
(1.00)
9p loss 0 (0%) 41 0.0033
(1.00) 		0.274
(1.00) 		0.183
(1.00) 		0.0128
(1.00) 		0.183
(1.00) 		0.0128
(1.00)
9q loss 0 (0%) 46 0.21
(1.00) 		0.493
(1.00) 		0.606
(1.00) 		0.667
(1.00) 		0.606
(1.00) 		0.667
(1.00)
10p loss 0 (0%) 34 0.115
(1.00) 		0.0772
(1.00) 		1
(1.00) 		0.34
(1.00) 		1
(1.00) 		0.34
(1.00)
10q loss 0 (0%) 32 0.0349
(1.00) 		0.0176
(1.00) 		0.0641
(1.00) 		0.0718
(1.00) 		0.0641
(1.00) 		0.0718
(1.00)
11p loss 0 (0%) 35 0.0322
(1.00) 		0.149
(1.00) 		0.41
(1.00) 		0.0647
(1.00) 		0.41
(1.00) 		0.0647
(1.00)
11q loss 0 (0%) 39 0.00273
(0.953) 		0.314
(1.00) 		0.183
(1.00) 		0.363
(1.00) 		0.183
(1.00) 		0.363
(1.00)
12q loss 0 (0%) 47 0.834
(1.00) 		0.856
(1.00) 		0.488
(1.00) 		0.488
(1.00)
13q loss 0 (0%) 29 0.0933
(1.00) 		0.343
(1.00) 		0.716
(1.00) 		0.56
(1.00) 		0.716
(1.00) 		0.56
(1.00)
14q loss 0 (0%) 36 0.0728
(1.00) 		0.274
(1.00) 		0.226
(1.00) 		0.15
(1.00) 		0.226
(1.00) 		0.15
(1.00)
15q loss 0 (0%) 43 0.0869
(1.00) 		0.2
(1.00) 		0.00843
(1.00) 		0.0136
(1.00) 		0.00843
(1.00) 		0.0136
(1.00)
16p loss 0 (0%) 43 0.412
(1.00) 		0.899
(1.00) 		0.343
(1.00) 		0.466
(1.00) 		0.343
(1.00) 		0.466
(1.00)
16q loss 0 (0%) 32 0.712
(1.00) 		0.0278
(1.00) 		0.688
(1.00) 		0.368
(1.00) 		0.688
(1.00) 		0.368
(1.00)
17p loss 0 (0%) 44 0.794
(1.00) 		0.243
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
17q loss 0 (0%) 47 0.834
(1.00) 		0.114
(1.00) 		0.573
(1.00) 		0.606
(1.00) 		0.573
(1.00) 		0.606
(1.00)
18p loss 0 (0%) 44 0.551
(1.00) 		0.243
(1.00) 		0.606
(1.00) 		0.667
(1.00) 		0.606
(1.00) 		0.667
(1.00)
18q loss 0 (0%) 42 0.74
(1.00) 		0.568
(1.00) 		0.606
(1.00) 		0.667
(1.00) 		0.606
(1.00) 		0.667
(1.00)
19q loss 0 (0%) 47 0.718
(1.00) 		0.351
(1.00) 		1
(1.00) 		1
(1.00)
20p loss 0 (0%) 47 0.221
(1.00) 		0.602
(1.00) 		0.343
(1.00) 		0.466
(1.00) 		0.343
(1.00) 		0.466
(1.00)
21q loss 0 (0%) 44 0.0191
(1.00) 		0.894
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
22q loss 0 (0%) 37 1
(1.00) 		0.473
(1.00) 		0.702
(1.00) 		0.817
(1.00) 		0.702
(1.00) 		0.817
(1.00)
Xq loss 0 (0%) 42 0.0627
(1.00) 		0.168
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

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

  • Number of patients = 52

  • Number of significantly arm-level cnvs = 65

  • Number of molecular subtypes = 6

  • 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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