Correlations between copy number and mRNAseq expression
Thymoma (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/C1319VC1
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 598, 1469.6, 2299, 2767, 3216, 3678.8, 4175, 4752, 5518.2, 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 123 120 119
Genes 24776 18301 15649

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
80777 CYB5B 16q22.1 0.7847 0 0
10425 ARIH2 3p21.31 0.7772 0 0
10294 DNAJA2 16q11.2 0.7706 0 0
9785 DHX38 16q22.2 0.7665 0 0
81631 MAP1LC3B 16q24.2 0.7574 0 0
7917 BAG6 6p21.33 0.7533 0 0
51094 ADIPOR1 1q32.1 0.7505 0 0
23300 ATMIN 16q23.2 0.7467 0 0
29097 CNIH4 1q42.11 0.7433 0 0
84276 NICN1 3p21.31 0.7405 0 0
6830 SUPT6H 17q11.2 0.7356 0 0
29117 BRD7 16q12.1 0.7334 0 0
5754 PTK7 6p21.1 0.7311 0 0
80222 TARS2 1q21.3 0.7291 0 0
9374 PPT2 6p21.32 0.7214 0 0
81577 GFOD2 16q22.1 0.7188 0 0
5432 POLR2C 16q21 0.7175 0 0
5089 PBX2 6p21.32 0.7154 0 0
3607 FOXK2 17q25.3 0.7132 0 0
59349 KLHL12 1q32.1 0.7112 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. The input file "THYM-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.