Correlations between copy number and mRNA expression
Rectum Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
Maintained by John Zhang (MD Anderson Cancer Center)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlations between copy number and mRNA expression. Broad Institute of MIT and Harvard. doi:10.7908/C1H99382
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 -0.07228, 0.008, 0.07373, 0.1409, 0.20575, 0.27506, 0.3453, 0.4236, 0.51868, 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 162 69 68
Genes 24174 17815 15702

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
RPL19 0.8789 0 0 6143 17q12 0.000 0.080
PIK3CB 0.8786 0 0 5291 3q22.3 -0.098 0.007
CNOT7 0.8693 0 0 29883 8p22 -0.087 -0.486
FBXL20 0.8371 0 0 84961 17q12 0.000 0.080
TSPAN14 0.8183 0 0 81619 10q23.1 -0.277 0.327
VPS37A 0.8169 0 0 137492 8p22 -0.087 -0.486
FAIM 0.814 0 0 55179 3q22.3 -0.098 0.007
PINX1 0.8073 0 0 54984 8p23.1 -0.123 -0.486
STARD3 0.7939 6.66133814775094e-16 4.56337605708362e-13 10948 17q12 0.000 0.080
DDX20 0.7934 6.66133814775094e-16 4.56337605708362e-13 11218 1p13.2 -0.291 -0.013
DSTN 0.7872 1.77635683940025e-15 1.10627298353542e-12 11034 20p12.1 1.005 -0.461
ANXA11 0.7853 2.22044604925031e-15 1.26760446030101e-12 311 10q22.3 -0.277 0.327
MCPH1 0.7824 3.33066907387547e-15 1.75514463733985e-12 79648 8p23.1 -0.123 -0.486
GTF2E2 0.7814 3.77475828372553e-15 1.77464624442141e-12 2961 8p12 -0.087 -0.495
COPS2 0.7809 3.99680288865056e-15 1.77464624442141e-12 9318 15q21.1 -0.279 0.001
POLR3D 0.7805 4.21884749357559e-15 1.77464624442141e-12 661 8p21.3 -0.087 -0.473
ZNF24 0.7803 4.44089209850063e-15 1.77464624442141e-12 7572 18q12.2 -0.306 -0.453
INTS9 0.7799 4.66293670342566e-15 1.77464624442141e-12 55756 8p21.1 -0.087 -0.473
ELP3 0.7767 7.105427357601e-15 2.56189533029256e-12 55140 8p21.1 -0.087 -0.473
C20orf72 0.7742 9.76996261670138e-15 3.34647577519466e-12 92667 20p11.23 1.005 -0.461
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

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