Correlations between copy number and mRNAseq expression
Brain Lower Grade Glioma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
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/C1CR5RDF
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 720.6, 1695, 2187, 2648, 3118, 3659, 4275, 4988.8, 5960.4, 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 220 220 218
Genes 23778 18364 18267

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
60313 GPBP1L1 1p34.1 0.8965 0 0
22826 DNAJC8 1p35.3 0.8841 0 0
998 CDC42 1p36.12 0.8742 0 0
23185 LARP4B 10p15.3 0.8684 0 0
7812 CSDE1 1p13.2 0.8681 0 0
56900 TMEM167B 1p13.3 0.8647 0 0
84919 PPP1R15B 1q32.1 0.8646 0 0
4898 NRD1 1p32.3 0.8643 0 0
51231 VRK3 19q13.33 0.8625 0 0
6429 SRSF4 1p35.3 0.8622 0 0
54455 FBXO42 1p36.13 0.8617 0 0
10489 LRRC41 1p34.1 0.8606 0 0
5690 PSMB2 1p34.3 0.8577 0 0
51441 YTHDF2 1p35.3 0.8561 0 0
23633 KPNA6 1p35.1 0.8555 0 0
56181 FAM54B 1p36.11 0.855 0 0
22887 FOXJ3 1p34.2 0.8537 0 0
51249 TMEM69 1p34.1 0.8521 0 0
8872 CDC123 10p13 0.8489 0 0
7268 TTC4 1p32.3 0.8471 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.