Esophageal Carcinoma: Correlation between copy number variations of arm-level result and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 38 arm-level results and molecular subtype 'METHLYATION_CNMF' across 20 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 38 arm-level results and 1 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

|  | Molecular subtypes | METHLYATION CNMF
| nCNV (%) | nWild-Type | Fisher's exact test
1q gain | 4 (20%) | 16 | 0.569 (1.00)
2p gain | 3 (15%) | 17 | 0.711 (1.00)
3p gain | 4 (20%) | 16 | 1 (1.00)
3q gain | 7 (35%) | 13 | 0.223 (1.00)
5p gain | 6 (30%) | 14 | 1 (1.00)
7p gain | 7 (35%) | 13 | 0.164 (1.00)
7q gain | 6 (30%) | 14 | 1 (1.00)
8p gain | 7 (35%) | 13 | 0.553 (1.00)
8q gain | 11 (55%) | 9 | 0.835 (1.00)
9q gain | 4 (20%) | 16 | 1 (1.00)
10p gain | 4 (20%) | 16 | 0.0788 (1.00)
12p gain | 9 (45%) | 11 | 0.0677 (1.00)
14q gain | 4 (20%) | 16 | 0.569 (1.00)
17p gain | 5 (25%) | 15 | 0.198 (1.00)
17q gain | 5 (25%) | 15 | 0.147 (1.00)
18p gain | 4 (20%) | 16 | 1 (1.00)
20p gain | 10 (50%) | 10 | 1 (1.00)
20q gain | 10 (50%) | 10 | 1 (1.00)
21q gain | 3 (15%) | 17 | 1 (1.00)
22q gain | 5 (25%) | 15 | 1 (1.00)
Xq gain | 4 (20%) | 16 | 1 (1.00)
3p loss | 7 (35%) | 13 | 0.655 (1.00)
4p loss | 6 (30%) | 14 | 0.51 (1.00)
4q loss | 5 (25%) | 15 | 0.198 (1.00)
5p loss | 4 (20%) | 16 | 0.569 (1.00)
5q loss | 4 (20%) | 16 | 0.569 (1.00)
6p loss | 6 (30%) | 14 | 0.51 (1.00)
6q loss | 3 (15%) | 17 | 1 (1.00)
9p loss | 3 (15%) | 17 | 0.344 (1.00)
10p loss | 4 (20%) | 16 | 1 (1.00)
10q loss | 3 (15%) | 17 | 0.711 (1.00)
11p loss | 3 (15%) | 17 | 0.711 (1.00)
13q loss | 7 (35%) | 13 | 0.223 (1.00)
16q loss | 4 (20%) | 16 | 1 (1.00)
18p loss | 6 (30%) | 14 | 0.408 (1.00)
18q loss | 7 (35%) | 13 | 1 (1.00)
21q loss | 10 (50%) | 10 | 0.443 (1.00)
22q loss | 3 (15%) | 17 | 0.518 (1.00)

Methods & Data
Input

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

- Molecular subtypes file = ESCA-TP.transferedmergedcluster.txt

- Number of patients = 20

- Number of significantly arm-level cnvs = 38

- Number of molecular subtypes = 1: 'METHLYATION_CNMF'

- 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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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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