Correlations between copy number and mRNAseq expression
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1X92958
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/C1X92958
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 730, 1653.2, 2674.8, 3322.4, 3929, 4534, 5178.2, 5860.8, 6657.4, 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 | 48 | 28 | 28
Genes | 24776 | 17576 | 15077

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
--- | --- | --- | --- | --- | ---
5194 | PEX13 | 2p16.1 | 0.8687 | 2.05811212516949e-09 | 3.10301565111804e-05
175 | AGA | 4q34.3 | 0.8382 | 2.59486694353939e-08 | 0.000391202140407998
79726 | WDR59 | 16q23.1 | 0.8375 | 2.73269702422141e-08 | 0.000411954076401377
8443 | GNPAT | 1q42.2 | 0.8327 | 3.87781682320565e-08 | 0.00058454210793002
55677 | IWS1 | 2q14.3 | 0.8267 | 5.92569100454909e-08 | 0.000893179405115685
10425 | ARIH2 | 3p21.31 | 0.8253 | 6.50746843078309e-08 | 0.000980805641887628
7323 | UBE2D3 | 4q24 | 0.8193 | 9.72969580459448e-08 | 0.00146636245471043
29117 | BRD7 | 16q12.1 | 0.8159 | 1.21696460908538e-07 | 0.00183396566589167
157556 | C8orf56 | 8q22.3 | 0.8131 | 0.00422912485453963 | 1
7360 | UGP2 | 2p15 | 0.8124 | 1.51685145333147e-07 | 0.00228574345502519
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 | 0.378589358095856
55249 | YY1AP1 | 1q22 | 0.8078 | 2.02156745121584e-07 | 0.00304609783549203
635 | BHMT | 5q14.1 | 0.8072 | 0.00853948021583473 | 1
3257 | HPS1 | 10q24.2 | 0.8037 | 2.60596201950847e-07 | 0.00392640297479341
1994 | ELAVL1 | 19p13.2 | 0.8029 | 2.73420626584198e-07 | 0.00411935516011752
123169 | LEO1 | 15q21.2 | 0.802 | 2.87697636380813e-07 | 0.00433416489207694
1874 | E2F4 | 16q22.1 | 0.8014 | 2.99176182050331e-07 | 0.00450679000640619
8846 | ALKBH1 | 14q24.3 | 0.8013 | 3.00875792280664e-07 | 0.00453209205912364

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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