Correlations between copy number and mRNAseq expression
Mesothelioma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlations between copy number and mRNAseq expression. Broad Institute of MIT and Harvard. doi:10.7908/C1ZK5FFQ

A TCGA sample is profiled to detect the copy number variations and expressions of genes. This pipeline attempts to correlate copy number and Rnaseq 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 RNAseq expression of the corresponding feature across patients. High positive/low negative correlation coefficients indicate that genomic alterations result in differences in the expressions of mRNAseq the genomic regions transcribe.


The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 996.9, 2302, 3071, 3758, 4438, 5109.4, 5814, 6552, 7394.1, 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 mRNAseq and number of samples in copy number and expression data sets and common to both

Category Copy number Expression Common
Sample 37 36 36
Genes 23778 18255 18160

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

Locus ID Gene Symbol Cytoband cor p-value q-value
342865 VSTM2B 19q12 0.9592 3.07516171793587e-06 0.0538531536651097
55862 ECHDC1 6q22.33 0.8827 1.0849099396637e-12 1.97019645042928e-08
93621 MRFAP1 4p16.1 0.8824 1.12709841459946e-12 2.04669801107116e-08
3954 LETM1 4p16.3 0.8776 2.13296047490985e-12 3.87302963034131e-08
10001 MED6 14q24.2 0.8773 2.21955787083061e-12 4.03005122606714e-08
64689 GORASP1 3p22.2 0.8749 3.02380342986908e-12 5.4900175072703e-08
10526 IPO8 12p11.21 0.8716 4.57101023698669e-12 8.29866908524934e-08
79892 MCMBP 10q26.11 0.8708 5.06394925992026e-12 9.19309348645925e-08
8314 BAP1 3p21.1 0.869 6.32027763458609e-12 1.14731999900641e-07
143187 VTI1A 10q25.2 0.8678 7.35744798419091e-12 1.33552395809033e-07
122553 TRAPPC6B 14q21.1 0.8653 9.90274529044655e-12 1.79744729766895e-07
80173 IFT74 9p21.2 0.8642 1.11712861183833e-11 2.02758843048656e-07
65981 CAPRIN2 12p11.21 0.863 1.28523858222707e-11 2.3325795028839e-07
81542 TMX1 14q22.1 0.8555 3.01612068653867e-11 5.47365582193038e-07
9878 TOX4 14q11.2 0.8552 3.11537462494016e-11 5.65347033187891e-07
53407 STX18 4p16.3 0.855 3.17914583547463e-11 5.76887803305226e-07
51409 HEMK1 3p21.2 0.8539 3.58748586393176e-11 6.50949310010418e-07
57862 ZNF410 14q24.3 0.8536 3.6978420325795e-11 6.70936458391225e-07
23256 SCFD1 14q12 0.8527 4.05884215126662e-11 7.3635514308279e-07
7323 UBE2D3 4q24 0.8527 4.05258049340773e-11 7.35259678918965e-07
Methods & Data

Gene level (TCGA Level III) mRNAseq expression data and copy number data of corresponding gene derived by GISTIC pipelinePearson 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.