Correlations between copy number and mRNAseq expression
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
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 (2015): Correlations between copy number and mRNAseq expression. Broad Institute of MIT and Harvard. doi:10.7908/C1765DHW

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 730, 1653.2, 2674.8, 3322.4, 3929, 4534, 5178.2, 5860.8, 6657.4, 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 48 28 28
Genes 24776 17576 15077

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
5194 PEX13 2p16.1 0.8687 2.05811212516949e-09 3.10301565111804e-05
175 AGA 4q34.3 0.8382 2.59486694353939e-08 0.000391202140407998
79726 WDR59 16q23.1 0.8375 2.73269702422141e-08 0.000411954076401377
8443 GNPAT 1q42.2 0.8327 3.87781682320565e-08 0.00058454210793002
55677 IWS1 2q14.3 0.8267 5.92569100454909e-08 0.000893179405115685
10425 ARIH2 3p21.31 0.8253 6.50746843078309e-08 0.000980805641887628
7323 UBE2D3 4q24 0.8193 9.72969580459448e-08 0.00146636245471043
29117 BRD7 16q12.1 0.8159 1.21696460908538e-07 0.00183396566589167
157556 C8orf56 8q22.3 0.8131 0.00422912485453963 1
7360 UGP2 2p15 0.8124 1.51685145333147e-07 0.00228574345502519
4101 MAGEA2 Xq28 0.8123 0.00430018191830372 1
402135 OR5K2 3q11.2 0.8115 0.00437221075269756 1
64922 LRRC19 9p21.2 0.8109 2.53101589848814e-05 0.378589358095856
55249 YY1AP1 1q22 0.8078 2.02156745121584e-07 0.00304609783549203
635 BHMT 5q14.1 0.8072 0.00853948021583473 1
3257 HPS1 10q24.2 0.8037 2.60596201950847e-07 0.00392640297479341
1994 ELAVL1 19p13.2 0.8029 2.73420626584198e-07 0.00411935516011752
123169 LEO1 15q21.2 0.802 2.87697636380813e-07 0.00433416489207694
1874 E2F4 16q22.1 0.8014 2.99176182050331e-07 0.00450679000640619
8846 ALKBH1 14q24.3 0.8013 3.00875792280664e-07 0.00453209205912364
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.