Correlations between copy number and mRNAseq expression
Lung Squamous Cell Carcinoma (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/C1QJ7FC2
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 1089.3, 1728, 2276, 2870, 3523.5, 4234, 4947, 5653.4, 6408, 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 416 347 345
Genes 23778 18529 18434

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
8500 PPFIA1 11q13.3 0.9185 0 0
8772 FADD 11q13.3 0.9088 0 0
220064 ORAOV1 11q13.3 0.8846 0 0
9070 ASH2L 8p11.23 0.8836 0 0
8451 CUL4A 13q34 0.8713 0 0
54904 WHSC1L1 8p11.23 0.8594 0 0
27257 LSM1 8p11.23 0.8577 0 0
55234 SMU1 9p21.1 0.8562 0 0
51193 ZNF639 3q26.33 0.8516 0 0
59343 SENP2 3q27.2 0.8446 0 0
8087 FXR1 3q26.33 0.8424 0 0
7415 VCP 9p13.3 0.8419 0 0
11212 PROSC 8p11.23 0.8416 0 0
83877 TM2D2 8p11.22 0.8351 0 0
55069 C7orf42 7q11.21 0.8339 0 0
9530 BAG4 8p11.23 0.8336 0 0
54165 DCUN1D1 3q26.33 0.8333 0 0
55588 MED29 19q13.2 0.8321 0 0
9878 TOX4 14q11.2 0.8295 0 0
55290 BRF2 8p11.23 0.8284 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.