Correlations between copy number and mRNAseq expression
Rectum Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1CJ8BKS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlations between copy number and mRNAseq expression. Broad Institute of MIT and Harvard. doi:10.7908/C1CJ8BKS
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 973, 2155, 2901, 3661, 4429, 5181, 5902, 6652, 7461, 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 162 51 50
Genes 23778 18106 18021

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
55617 TASP1 20p12.1 0.9258 0 0
8725 URI1 19q12 0.9255 0 0
51340 CRNKL1 20p11.23 0.9251 0 0
55968 NSFL1C 20p13 0.9251 0 0
10775 POP4 19q12 0.9201 0 0
55246 CCDC25 8p21.1 0.918 0 0
5786 PTPRA 20p13 0.9074 0 0
208 AKT2 19q13.2 0.9071 0 0
6629 SNRPB2 20p12.1 0.9055 0 0
92667 C20orf72 20p11.23 0.9052 0 0
9491 PSMF1 20p13 0.897 0 0
8760 CDS2 20p12.3 0.8964 0 0
64412 GZF1 20p11.21 0.8944 0 0
27131 SNX5 20p11.23 0.8927 0 0
83636 C19orf12 19q12 0.8924 0 0
91782 CHMP7 8p21.3 0.8924 0 0
22888 UBOX5 20p13 0.8922 0 0
51605 TRMT6 20p12.3 0.892 0 0
26133 TRPC4AP 20q11.22 0.8918 0 0
8881 CDC16 13q34 0.8911 0 0
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.

Correlation across sample

Pairwise correlations between the log2 copy numbers and expressions of each gene across samples were calculated using Pearson correlation.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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