Skin Cutaneous Melanoma: Correlations between copy number and mRNAseq expression
(BRAF_Hotspot_Mutants 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 1008, 1912, 2541, 3129, 3728.5, 4354, 4986.7, 5652, 6403, 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 99 99 99
Genes 23778 18144 18052

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
54476 RNF216 7p22.1 0.8375 0 0
54926 UBE2R2 9p13.3 0.8303 0 0
5780 PTPN9 15q24.2 0.8199 0 0
80135 RPF1 1p22.3 0.8156 0 0
60685 ZFAND3 6p21.2 0.8055 0 0
1211 CLTA 9p13.3 0.8045 0 0
5528 PPP2R5D 6p21.1 0.8029 0 0
3550 IK 5q31.3 0.8006 0 0
5537 PPP6C 9q33.3 0.7998 0 0
9861 PSMD6 3p14.1 0.7989 0 0
23070 FTSJD2 6p21.2 0.7967 0 0
9798 IST1 16q22.2 0.7948 0 0
129685 TAF8 6p21.1 0.7945 0 0
2547 XRCC6 22q13.2 0.7942 0 0
5546 PRCC 1q23.1 0.7927 0 0
2787 GNG5 1p22.3 0.791 0 0
55069 C7orf42 7q11.21 0.7888 0 0
23386 NUDCD3 7p13 0.7876 0 0
8812 CCNK 14q32.2 0.7868 0 0
26263 FBXO22 15q24.2 0.7861 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