Correlations between copy number and mRNAseq expression
Lung Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1RN35XR
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/C1RN35XR
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 1049, 1687.8, 2238.7, 2811, 3422.5, 4065, 4720, 5395, 6141, 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 493 393 391
Genes 23778 18310 18220

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
4848 CNOT2 12q15 0.8489 0 0
9070 ASH2L 8p11.23 0.846 0 0
6729 SRP54 14q13.2 0.8437 0 0
8451 CUL4A 13q34 0.8381 0 0
8725 URI1 19q12 0.8232 0 0
83636 C19orf12 19q12 0.8202 0 0
11336 EXOC3 5p15.33 0.8095 0 0
10775 POP4 19q12 0.7991 0 0
8881 CDC16 13q34 0.7988 0 0
79648 MCPH1 8p23.1 0.7983 0 0
11212 PROSC 8p11.23 0.7958 0 0
55756 INTS9 8p21.1 0.7923 0 0
55958 KLHL9 9p21.3 0.7921 0 0
134218 DNAJC21 5p13.2 0.7909 0 0
7572 ZNF24 18q12.2 0.7894 0 0
10778 ZNF271 18q12.2 0.789 0 0
122553 TRAPPC6B 14q21.1 0.7876 0 0
55341 LSG1 3q29 0.7858 0 0
54994 C20orf11 20q13.33 0.7835 0 0
91782 CHMP7 8p21.3 0.7831 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.

Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle