Correlations between copy number and mRNAseq expression
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
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 (2016): Correlations between copy number and mRNAseq expression. Broad Institute of MIT and Harvard. doi:10.7908/C1T72GT7
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 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.

Summary

The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 725, 1716.6, 2482, 3022.2, 3561, 4115, 4684, 5340, 6119, 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 mRNAseq and number of samples in copy number and expression data sets and common to both

Category Copy number Expression Common
Sample 48 48 48
Genes 24776 17683 15159

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
22916 NCBP2 3q29 0.8479 2.88657986402541e-14 4.37576641587611e-10
9218 VAPA 18p11.22 0.84 8.4821039081362e-14 1.28571731039528e-09
9474 ATG5 6q21 0.8299 3.08642000845794e-13 4.67808680681969e-09
4087 SMAD2 18q21.1 0.8133 2.1582735598713e-12 3.27107940734095e-08
9150 CTDP1 18q23 0.8104 2.96518365416887e-12 4.49373582789292e-08
205564 SENP5 3q29 0.8098 3.1774582964772e-12 4.81512030248155e-08
79648 MCPH1 8p23.1 0.8076 4.04387634489467e-12 6.12768582541889e-08
51031 GLOD4 17p13.3 0.8051 5.29620791667185e-12 8.02481423534118e-08
29888 STRN4 19q13.32 0.8005 8.59490256743811e-12 1.30221368799255e-07
5194 PEX13 2p16.1 0.7953 1.45166101361838e-11 2.19926643563184e-07
7917 BAG6 6p21.33 0.7931 1.81987758196556e-11 2.75693254891962e-07
57805 KIAA1967 8p21.3 0.7886 2.83608692086545e-11 4.29610446772699e-07
10575 CCT4 2p15 0.7815 5.57691670621807e-11 8.44735573490851e-07
10939 AFG3L2 18p11.21 0.7811 5.75646197376045e-11 8.71873730545758e-07
8443 GNPAT 1q42.2 0.7785 7.34778904387667e-11 1.11282265069512e-06
54965 PIGX 3q29 0.7744 1.06467723526293e-10 1.61234720508219e-06
51447 IP6K2 3p21.31 0.7652 2.40337527657175e-10 3.6394311813126e-06
7323 UBE2D3 4q24 0.7573 4.69906780153906e-10 7.11532846509044e-06
9984 THOC1 18p11.32 0.7572 4.72824890351831e-10 7.15904166481707e-06
55677 IWS1 2q14.3 0.7569 4.82402562340667e-10 7.3035747938377e-06
Methods & Data
Input

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. The input file "DLBC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt " is generated in the pipeline mRNAseq_Preprocess in the stddata run.

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.