Correlations between copy number and mRNA expression
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1NC5ZVF
Maintained by John Zhang (MD Anderson Cancer Center)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlations between copy number and mRNA expression. Broad Institute of MIT and Harvard. doi:10.7908/C1NC5ZVF
Overview
Introduction

A TCGA sample is profiled to detect the copy number variations and expressions of genes. This pipeline attempts to correlate copy number and expression data of genes across samples to determine if the copy number variations also result in differential expressions. This report contains the calculated correlation coefficients based on measurements of genomic copy number (log2) values and intensity of the expressions of the corresponding feature across patients. High positive/low negative correlation coefficients indicate that genomic alterations result in differences in the expressions of mRNA the genomic regions transcribe.

Summary

The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 0.0155, 0.0651, 0.1219, 0.2006, 0.2915, 0.3837, 0.4583, 0.531, 0.6006, respectively.

Results
Correlation results

Number of genes and samples used for the calculation are shown in Table 1. Figure 1 shows the distribution of calculated correlation coefficients and quantile-quantile plot of the calculated correlation coefficients against a normal distribution. Table 2 shows the top 20 features ordered by the value of correlation coefficients.

Table 1. Counts of mRNA and number of samples in copy number and expression data sets and common to both

Category | Copy number | Expression | Common
--- | --- | --- | ---
Sample | 569 | 569 | 550
Genes | 24174 | 18633 | 16221

Figure 1. Summary figures. Left: histogram showing the distribution of the calculated correlations across samples for all Genes. Right: QQ plot of the calculated correlations across samples. The QQ plot is used to plot the quantiles of the calculated correlation coefficients against that derived from a normal distribution. Points deviating from the blue line indicate deviation from normality.

Table 2. Get Full Table Top 20 features (defined by the feature column) ranked by correlation coefficients

feature | r | p-value | q-value | chrom | start | end | geneid
--- | --- | --- | --- | --- | --- | --- | ---
PAF1 | 0.8565 | 0 | 0 | 54623 | 19q13.2 | 0.046 | 2.662
TBP | 0.8348 | 0 | 0 | 6908 | 6q27 | -0.792 | -0.367
ASCC2 | 0.8324 | 0 | 0 | 84164 | 22q12.2 | -0.715 | 0.033
MED29 | 0.8101 | 0 | 0 | 55588 | 19q13.2 | 0.046 | 2.662
RANBP3 | 0.8073 | 0 | 0 | 8498 | 19p13.3 | -0.698 | -0.643
TIMM50 | 0.807 | 0 | 0 | 92609 | 19q13.2 | 0.046 | 2.662
MTMR3 | 0.8038 | 0 | 0 | 8897 | 22q12.2 | -0.715 | 0.033
CUL4A | 0.803 | 0 | 0 | 8451 | 13q34 | 0.039 | -0.261
FAM120B | 0.802 | 0 | 0 | 84498 | 6q27 | -0.792 | -0.367
SUPT5H | 0.8014 | 0 | 0 | 6829 | 19q13.2 | 0.046 | 2.662
ANKRD27 | 0.8003 | 0 | 0 | 84079 | 19q13.11 | 0.008 | 0.527
CCDC130 | 0.7995 | 0 | 0 | 81576 | 19p13.2 | 0.008 | -0.234
TOX4 | 0.7974 | 0 | 0 | 9878 | 14q11.2 | 0.014 | 1.633
C18orf8 | 0.7946 | 0 | 0 | 29919 | 18q11.2 | -0.027 | 3.657
KIAA1967 | 0.7932 | 0 | 0 | 57805 | 8p21.3 | -0.081 | -0.633
TYK2 | 0.793 | 0 | 0 | 7297 | 19p13.2 | 0.008 | -0.234
AKT2 | 0.7915 | 0 | 0 | 208 | 19q13.2 | 0.046 | 3.578
CNOT2 | 0.79 | 0 | 0 | 4848 | 12q15 | 0.003 | 0.119
ZNF623 | 0.7894 | 0 | 0 | 9831 | 8q24.3 | 0.040 | 0.370
MBD1 | 0.7866 | 0 | 0 | 4152 | 18q21.1 | -0.027 | -0.340

Methods & Data
Input

Gene level (TCGA Level III) expression data and copy number data of the corresponding loci derived by using the CNTools package of Bioconductor were used for the calculations. Pearson correlation coefficients were calculated for each pair of genes shared by the two data sets across all the samples that were common.

Correlation across sample

Pairwise correlations between the log2 copy numbers and expressions of each gene across samples were calculated using Pearson correlation.

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle