Glioblastoma Multiforme: Correlations between copy number and mRNAseq expression
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 953.4, 1848.8, 2387.2, 2921, 3435, 3984, 4584.8, 5254, 6118.6, 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 563 154 148
Genes 23778 18190 18095

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
4193 MDM2 12q15 0.9336 0 0
92979 MARCH9 12q14.1 0.9098 0 0
23480 SEC61G 7p11.2 0.9001 0 0
1019 CDK4 12q14.1 0.8971 0 0
84919 PPP1R15B 1q32.1 0.8968 0 0
10540 DCTN2 12q13.3 0.8966 0 0
10956 OS9 12q13.3 0.8952 0 0
10102 TSFM 12q14.1 0.8947 0 0
79837 PIP4K2C 12q13.3 0.8855 0 0
55915 LANCL2 7p11.2 0.8788 0 0
51373 MRPS17 7p11.2 0.8785 0 0
55234 SMU1 9p21.1 0.8738 0 0
6302 TSPAN31 12q14.1 0.8717 0 0
4234 METTL1 12q14.1 0.8714 0 0
115557 ARHGEF25 12q13.3 0.8708 0 0
10106 CTDSP2 12q14.1 0.8697 0 0
25895 METTL21B 12q14.1 0.8694 0 0
908 CCT6A 7p11.2 0.8641 0 0
196403 DTX3 12q13.3 0.8635 0 0
55763 EXOC1 4q12 0.8604 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.