Correlations between copy number and mRNAseq expression
Stomach Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
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 (2013): Correlations between copy number and mRNAseq expression. Broad Institute of MIT and Harvard. doi:10.7908/C1X63K6C

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.


The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 1118.2, 2319.4, 3065.6, 3788, 4531, 5253.2, 6000.4, 6791, 7664.8, respectively.

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 237 43 43
Genes 23778 19368 19263

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
830 CAPZA2 7q31.2 0.9454 0 0
6605 SMARCE1 17q21.2 0.9444 0 0
54994 C20orf11 20q13.33 0.932 0 0
6780 STAU1 20q13.13 0.9231 0 0
10775 POP4 19q12 0.9209 0 0
84060 RBM48 7q21.2 0.9207 0 0
84299 MIEN1 17q12 0.9127 0 0
9070 ASH2L 8p11.23 0.9109 0 0
137492 VPS37A 8p22 0.9106 0 0
79058 ASPSCR1 17q25.3 0.9095 0 0
10210 TOPORS 9p21.1 0.9079 0 0
10564 ARFGEF2 20q13.13 0.8996 2.22044604925031e-16 1.32201339535069e-13
2029 ENSA 1q21.3 0.8984 4.44089209850063e-16 2.26630867774404e-13
91782 CHMP7 8p21.3 0.8956 4.44089209850063e-16 2.26630867774404e-13
3858 KRT10 17q21.2 0.8938 8.88178419700125e-16 3.96604018605207e-13
8725 URI1 19q12 0.8935 8.88178419700125e-16 3.96604018605207e-13
55610 CCDC132 7q21.3 0.8907 1.33226762955019e-15 5.00973497185525e-13
4799 NFX1 9p13.3 0.8903 1.33226762955019e-15 5.00973497185525e-13
6873 TAF2 8q24.12 0.8902 1.33226762955019e-15 5.00973497185525e-13
4848 CNOT2 12q15 0.8878 2.22044604925031e-15 7.5543622591468e-13
Methods & Data

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.