Ovarian Serous Cystadenocarcinoma: Correlations between copy number and mRNAseq expression
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/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 1097.9, 1793, 2459, 3195.6, 3989.5, 4790, 5511.3, 6130, 6773, 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 558 207 202
Genes 22749 18729 17900

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
83636 C19orf12 19q12 0.9034 0 0
54623 PAF1 19q13.2 0.9021 0 0
55588 MED29 19q13.2 0.8908 0 0
8725 URI1 19q12 0.8748 0 0
51283 BFAR 16p13.12 0.8678 0 0
91782 CHMP7 8p21.3 0.8676 0 0
84164 ASCC2 22q12.2 0.8674 0 0
6829 SUPT5H 19q13.2 0.8651 0 0
3845 KRAS 12p12.1 0.8634 0 0
4848 CNOT2 12q15 0.863 0 0
126526 C19orf47 19q13.2 0.8595 0 0
221955 DAGLB 7p22.1 0.857 0 0
55095 SAMD4B 19q13.2 0.8566 0 0
208 AKT2 19q13.2 0.855 0 0
9441 MED26 19p13.11 0.8543 0 0
10775 POP4 19q12 0.8523 0 0
54850 FBXL12 19p13.2 0.8522 0 0
112398 EGLN2 19q13.2 0.8493 0 0
125950 RAVER1 19p13.2 0.8487 0 0
5704 PSMC4 19q13.2 0.8482 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.