Colon Adenocarcinoma: 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 809.1, 1659.2, 2184, 2680, 3163, 3664, 4165.7, 4737.8, 5498.9, 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 413 192 184
Genes 23778 17848 17762

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
51507 C20orf43 20q13.31 0.8541 0 0
91782 CHMP7 8p21.3 0.8449 0 0
5786 PTPRA 20p13 0.8437 0 0
54994 C20orf11 20q13.33 0.841 0 0
54915 YTHDF1 20q13.33 0.8397 0 0
9675 TTI1 20q11.23 0.8271 0 0
57136 C20orf3 20p11.21 0.8263 0 0
25980 C20orf4 20q11.23 0.8225 0 0
23514 KIAA0146 8q11.21 0.8189 0 0
9491 PSMF1 20p13 0.8185 0 0
6874 TAF4 20q13.33 0.8164 0 0
337867 UBAC2 13q32.3 0.8121 0 0
57805 KIAA1967 8p21.3 0.8099 0 0
26090 ABHD12 20p11.21 0.8058 0 0
128869 PIGU 20q11.22 0.8041 0 0
81572 PDRG1 20q11.21 0.8021 0 0
57325 CSRP2BP 20p11.23 0.7938 0 0
55968 NSFL1C 20p13 0.7936 0 0
55661 DDX27 20q13.13 0.7924 0 0
203069 R3HCC1 8p21.3 0.7922 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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