Correlations between copy number and mRNA expression

Lung Adenocarcinoma (MOLECULAR_NONSMOKER)

07 February 2013 | awg_luad__2013_02_07

Maintainer Information

Citation Information

Maintained by John Zhang (MD Anderson Cancer Center)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlations between copy number and mRNA expression. Broad Institute of MIT and Harvard. doi:10.7908/C1F47M7Q

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 expression 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 intensity of the expressions of the corresponding feature across patients. High positive/low negative correlation coefficients indicate that genomic alterations result in differences in the expressions of mRNA the genomic regions transcribe.

Summary

The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.31188, -0.1302, 0.0108, 0.13158, 0.2402, 0.34752, 0.4539, 0.5627, 0.68836, 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 mRNA and number of samples in copy number and expression data sets and common to both

Category	Copy number	Expression	Common
Sample	81	9	9
Genes	29390	17815	15551

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

feature	r	p-value	q-value	chrom	start	end	geneid
C14orf166	0.9853	1.25250272442479e-06	0.013332739796438	14	51525943	51541163	51637
PSMC6	0.9672	2.03464186316893e-05	0.0627944078570079	14	52243668	52264466	5706
USF2	0.9651	2.52606079973461e-05	0.0627944078570079	19	40451736	40462558	7392
GARNL1	0.9633	3.01833536375806e-05	0.0627944078570079	14	35077309	35348183	253959
ZNF655	0.9615	3.56374468546417e-05	0.0627944078570079	7	98993981	99012012	79027
CHD9	0.9602	3.97332201445e-05	0.0627944078570079	16	51747339	51918283	80205
ATP5E	0.9589	4.43466397321846e-05	0.0627944078570079	20	57037128	57040817	514
HEBP2	0.9575	5.00511425123307e-05	0.0627944078570079	6	138767029	138776275	23593
DNAJB2	0.9568	5.30912260408023e-05	0.0627944078570079	2	219852342	219859866	3300
LNX2	0.9509	8.23304581247797e-05	0.0720864369180551	13	27018050	27053940	222484
ZNF408	0.9505	8.4769446073718e-05	0.0720864369180551	11	46678944	46684037	79797
YIPF4	0.9493	9.19557282714756e-05	0.0720864369180551	2	32356535	32385145	84272
NSMCE1	0.9455	0.000117660661807406	0.0720864369180551	16	27143825	27176376	197370
PARP11	0.9451	0.000120673755628076	0.0720864369180551	12	3788288	3852863	57097
PPIL5	0.9431	0.000136581024575699	0.0720864369180551	14	49135165	49151140	122769
FKBP3	0.943	0.000137625896316163	0.0720864369180551	14	44654859	44674272	2287
TOPBP1	0.9429	0.000138306799744026	0.0720864369180551	3	134802177	134863380	11073
DDHD1	0.9425	0.000141859232203778	0.0720864369180551	14	52582491	52689750	80821
SLC12A7	0.9421	0.000144863753712254	0.0720864369180551	5	1103499	1165109	10723
LSMD1	0.9411	0.0001541076330831	0.0720864369180551	17	7700728	7701897	84316

Methods & Data

Input

Gene level (TCGA Level III) expression data and copy number data of the corresponding loci derived by using the CNTools package of Bioconductor were used for the calculations. Pearson 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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