Correlations between copy number and mRNA expression
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
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/C1X065S3

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.


The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.17847, -0.0653, 0.0121, 0.08052, 0.1431, 0.20918, 0.27931, 0.3647, 0.47984, respectively.

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 527 72 30
Genes 24174 17814 15704

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
ZNF193 0.8861 7.44937445062988e-11 7.60629854703389e-07 7746 6p22.1 -0.013 0.000
FBXO42 0.8427 5.16365483704817e-09 1.26506967112289e-05 54455 1p36.13 -0.001 0.002
RPAIN 0.8405 6.19939544144188e-09 1.26506967112289e-05 84268 17p13.2 0.002 0.002
TBP 0.839 6.96874580263795e-09 1.26506967112289e-05 6908 6q27 -0.013 -0.003
TMUB1 0.8382 7.43382155832251e-09 1.26506967112289e-05 83590 7q36.1 0.053 -0.002
MAP3K7 0.8346 9.91858950527558e-09 1.44678980271815e-05 6885 6q15 -0.013 0.000
CDC5L 0.8276 1.68614957551938e-08 2.15208625089158e-05 988 6p21.1 -0.013 0.000
CSNK2B 0.8232 2.34323052072938e-08 2.43637958663008e-05 1460 6p21.33 -0.013 0.000
IFI44L 0.8223 2.50225475895149e-08 2.43637958663008e-05 10964 1p31.1 -0.001 0.002
RING1 0.8216 2.62472661383129e-08 2.43637958663008e-05 6015 6p21.32 -0.013 0.000
IFI44 0.8109 5.54130870078495e-08 4.57520916414837e-05 10561 1p31.1 -0.001 0.002
UBR2 0.8101 5.82506456403564e-08 4.57520916414837e-05 23304 6p21.1 -0.013 0.000
FASTK 0.8045 8.43254865934284e-08 5.68245864724399e-05 10922 7q36.1 0.053 -0.002
GNL2 0.8026 9.52888945526809e-08 5.68245864724399e-05 29889 1p34.3 -0.001 0.002
PRPF38A 0.8026 9.52638883333634e-08 5.68245864724399e-05 84950 1p32.3 -0.001 0.002
CDC40 0.8013 1.03460028544333e-07 5.68245864724399e-05 51362 6q21 -0.013 0.000
TBCC 0.8009 1.06681918854434e-07 5.68245864724399e-05 6903 6p21.1 -0.013 0.000
C6ORF62 0.8002 1.11304498506826e-07 5.68245864724399e-05 81688 6p22.3 -0.013 0.000
GTF2E2 0.7984 1.24582162364106e-07 6.05745410383526e-05 2961 8p12 -0.008 -0.001
MAD2L1BP 0.7961 1.43843635669327e-07 6.67608001085956e-05 9587 6p21.1 -0.013 0.000
Methods & Data

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.