Correlations between copy number and mRNAseq expression
Pancreatic Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_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/C1DR2SXR

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 891.3, 2152, 2845, 3462, 4051, 4620, 5232.1, 5910, 6750, 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 81 56 55
Genes 23778 18507 18414

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
6882 TAF11 6p21.31 0.9415 0 0
4848 CNOT2 12q15 0.9324 0 0
54902 TTC19 17p12 0.9166 0 0
79602 ADIPOR2 12p13.33 0.9074 0 0
221833 SP8 7p21.1 0.9055 5.73983999441197e-07 0.0101755883420935
64771 C6orf106 6p21.31 0.8909 0 0
5908 RAP1B 12q15 0.8889 0 0
11052 CPSF6 12q15 0.8861 0 0
125150 ZSWIM7 17p12 0.8717 0 0
11333 PDAP1 7q22.1 0.8676 0 0
79591 C10orf76 10q24.32 0.8609 0 0
7551 ZNF3 7q22.1 0.8556 0 0
11011 TLK2 17q23.2 0.8515 2.22044604925031e-16 4.08628686443535e-12
8089 YEATS4 12q15 0.8504 2.22044604925031e-16 4.08628686443535e-12
11325 DDX42 17q23.3 0.8502 2.22044604925031e-16 4.08628686443535e-12
144699 FBXL14 12p13.33 0.85 2.22044604925031e-16 4.08628686443535e-12
11165 NUDT3 6p21.31 0.8486 4.44089209850063e-16 8.1707973720313e-12
10552 ARPC1A 7q22.1 0.8436 6.66133814775094e-16 1.22555299242322e-11
57122 NUP107 12q15 0.8417 8.88178419700125e-16 1.63398183872232e-11
6829 SUPT5H 19q13.2 0.8409 8.88178419700125e-16 1.63398183872232e-11
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.