Correlations between copy number and mRNAseq expression

Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlations between copy number and mRNAseq expression. Broad Institute of MIT and Harvard. doi:10.7908/C19Z93M7

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 765.2, 1733, 2905, 3572.8, 4202, 4827, 5499, 6223.6, 7058.8, 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	28	28	28
Genes	23778	17576	17493

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
266722	HS6ST3	13q32.1	0.9397	1.73920414119344e-05	0.302517168319187
5194	PEX13	2p16.1	0.8687	2.05811212516949e-09	3.60025554055898e-05
175	AGA	4q34.3	0.8382	2.59486694353939e-08	0.00045389412576391
79726	WDR59	16q23.1	0.8375	2.73269702422141e-08	0.000477976036506567
8443	GNPAT	1q42.2	0.8327	3.87781682320565e-08	0.000678230162378668
55677	IWS1	2q14.3	0.8267	5.92569100454909e-08	0.00103634409978559
10425	ARIH2	3p21.31	0.8253	6.50746843078309e-08	0.00113802607917535
7323	UBE2D3	4q24	0.8193	9.72969580459448e-08	0.00170143190534944
29117	BRD7	16q12.1	0.8159	1.21696460908538e-07	0.0021279843154467
157556	C8orf56	8q22.3	0.8131	0.00422912485453963	1
7360	UGP2	2p15	0.8124	1.51685145333147e-07	0.00265221476615007
4101	MAGEA2	Xq28	0.8123	0.00430018191830372	1
402135	OR5K2	3q11.2	0.8115	0.00437221075269756	1
64922	LRRC19	9p21.2	0.8109	2.53101589848814e-05	0.439561531090436
55249	YY1AP1	1q22	0.8078	2.02156745121584e-07	0.00353450853170578
635	BHMT	5q14.1	0.8072	0.00853948021583473	1
3257	HPS1	10q24.2	0.8037	2.60596201950847e-07	0.00455600339870665
1994	ELAVL1	19p13.2	0.8029	2.73420626584198e-07	0.00477993939394494
123169	LEO1	15q21.2	0.802	2.87697636380813e-07	0.00502924238157298
1874	E2F4	16q22.1	0.8014	2.99176182050331e-07	0.00522959966223979

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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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