Correlations between copy number and miR expression
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by John Zhang (MD Anderson Cancer Center)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlations between copy number and miR expression. Broad Institute of MIT and Harvard. doi:10.7908/C16W98W8
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 miRNA the genomic regions transcribe.

Summary

The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.0361, -0.01828, 0.00444, 0.01676, 0.0393, 0.07706, 0.13056, 0.23136, 0.35344, 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 miR and number of samples in copy number and expression data sets and common to both

Category Copy number Expression Common
Sample 569 568 547
miR 357 822 357

Figure 1.  Summary figures. Left: histogram showing the distribution of the calculated correlations across samples for all miR. 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
HSA-MIR-30E 0.6731 0 0 -899 1p34.2 0.062 0.505
HSA-MIR-27A 0.6264 0 0 -691 19p13.13 0.008 -0.234
HSA-MIR-23A 0.6103 0 0 -691 19p13.13 0.008 -0.234
HSA-MIR-30B 0.6079 0 0 -1621 8q24.22 0.040 0.370
HSA-MIR-30D 0.5896 0 0 -1621 8q24.22 0.040 0.370
HSA-MIR-641 0.5123 0 0 -896 19q13.2 0.046 3.578
HSA-MIR-185 0.5103 0 0 -737 22q11.21 -0.715 0.033
HSA-MIR-17 0.5089 0 0 -1286 13q31.3 0.005 -0.261
HSA-MIR-181D 0.4893 0 0 -691 19p13.13 0.008 -0.234
HSA-MIR-200C 0.4769 0 0 -638 12p13.31 0.015 0.347
HSA-MIR-484 0.4744 0 0 -705 16p13.11 -0.451 -0.304
HSA-MIR-186 0.4502 0 0 -1130 1p31.1 0.038 -0.291
HSA-LET-7B 0.4443 0 0 -939 22q13.31 -0.715 -0.362
HSA-MIR-148B 0.4411 0 0 -1002 12q13.13 0.003 0.119
HSA-MIR-106B 0.4384 0 0 -1345 7q22.1 0.010 -0.274
HSA-MIR-19A 0.4315 0 0 -1286 13q31.3 0.005 -0.261
HSA-MIR-33A 0.4292 0 0 -907 22q13.2 -0.715 -0.362
HSA-MIR-20A 0.4233 0 0 -1286 13q31.3 0.005 -0.261
HSA-MIR-25 0.4082 0 0 -1345 7q22.1 0.010 -0.274
HSA-MIR-182 0.4054 0 0 -1572 7q32.2 0.004 0.094
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

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.