Correlations between copy number and mRNAseq expression
Thyroid Adenocarcinoma
01 July 2013  |  awg_thca__2013_07_01
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 (2013): Correlations between copy number and mRNAseq expression. Broad Institute of MIT and Harvard. doi:10.7908/C1J1018C
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 427, 1175, 1746, 2053, 2354, 2686, 3052, 3542, 4197.5, 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 502 490 488
Genes 23778 18003 17916

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
2547 XRCC6 22q13.2 0.7578 0 0
158 ADSL 22q13.1 0.7492 0 0
10454 TAB1 22q13.1 0.7476 0 0
24144 TFIP11 22q12.1 0.7316 0 0
6767 ST13 22q13.2 0.7183 0 0
23760 PITPNB 22q12.1 0.7106 0 0
83606 C22orf13 22q11.23 0.7091 0 0
51386 EIF3L 22q13.1 0.7089 0 0
83746 L3MBTL2 22q13.2 0.7077 0 0
51493 C22orf28 22q12.3 0.7006 0 0
6598 SMARCB1 22q11.23 0.6894 0 0
8664 EIF3D 22q12.3 0.6884 0 0
25771 TBC1D22A 22q13.31 0.6853 0 0
9342 SNAP29 22q11.21 0.6832 0 0
9701 PPP6R2 22q13.33 0.6798 0 0
25814 ATXN10 22q13.31 0.6752 0 0
4733 DRG1 22q12.2 0.6751 0 0
56478 EIF4ENIF1 22q12.2 0.6679 0 0
10478 SLC25A17 22q13.2 0.6621 0 0
84844 PHF5A 22q13.2 0.659 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.