Brain Lower Grade Glioma: 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 780, 1903, 2437, 2972, 3502, 4086, 4747, 5516, 6518, 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 180 110 109
Genes 23778 18308 18211

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 0.9187 0 0
22826 DNAJC8 1p35.3 0.9094 0 0
51231 VRK3 19q13.33 0.9044 0 0
10576 CCT2 12q15 0.8969 0 0
4898 NRD1 1p32.3 0.8933 0 0
51249 TMEM69 1p34.1 0.8933 0 0
23480 SEC61G 7p11.2 0.8906 0 0
92979 MARCH9 12q14.1 0.8902 0 0
23185 LARP4B 10p15.3 0.8865 0 0
5690 PSMB2 1p34.3 0.8833 0 0
7812 CSDE1 1p13.2 0.8825 0 0
908 CCT6A 7p11.2 0.8825 0 0
23560 GTPBP4 10p15.3 0.8812 0 0
6429 SRSF4 1p35.3 0.8797 0 0
7268 TTC4 1p32.3 0.8797 0 0
8872 CDC123 10p13 0.8787 0 0
56181 FAM54B 1p36.11 0.8765 0 0
51441 YTHDF2 1p35.3 0.8762 0 0
6302 TSPAN31 12q14.1 0.876 0 0
998 CDC42 1p36.12 0.8754 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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