Uterine Corpus Endometrioid Carcinoma: Correlations between copy number and mRNA expression
Maintained by John Zhang (MD Anderson Cancer Center)
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 -0.10396, -0.01376, 0.05256, 0.10998, 0.1701, 0.2327, 0.29614, 0.3686, 0.4651, 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 428 54 53
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
LCMT1 0.8092 2.26485497023532e-13 1.63387525534863e-09 16 25030548 25097052 51451
POFUT1 0.7913 1.7705836796722e-12 5.62779254620084e-09 20 30259357 30290128 23509
RAF1 0.7887 2.34035013590983e-12 5.62779254620084e-09 3 12600108 12680678 5894
MAP2K4 0.7752 9.48396916555794e-12 1.71044313496203e-08 17 11864860 11987776 6416
B4GALT3 0.7715 1.36708422360243e-11 1.97243983767264e-08 1 159407725 159413938 8703
RPL32 0.7679 1.94280147525205e-11 2.33590766898666e-08 3 12851444 12858081 6161
PREP 0.7634 2.99051894359081e-11 2.69670965273611e-08 6 105832199 105957662 5550
UBA52 0.763 3.10007575166082e-11 2.69670965273611e-08 19 18543668 18547050 7311
ATAD1 0.7616 3.5627722994036e-11 2.69670965273611e-08 10 89502855 89567897 84896
YWHAZ 0.7609 3.79438702680091e-11 2.69670965273611e-08 8 102000090 102034745 7534
UBL5 0.76 4.11195522076468e-11 2.69670965273611e-08 19 9799614 9801791 59286
PLAGL2 0.7591 4.497535677217e-11 2.703783225867e-08 20 30243968 30259192 5326
ARPC5 0.7573 5.29123411752153e-11 2.89043745540572e-08 1 181861955 181871608 10092
WHSC2 0.7563 5.80284709172929e-11 2.89043745540572e-08 4 1954248 1980547 7469
DVL3 0.7555 6.24540419380537e-11 2.89043745540572e-08 3 185355978 185374008 1857
SUMO2 0.7552 6.41069419771156e-11 2.89043745540572e-08 17 70675420 70690693 6613
CSNK2A1 0.7542 6.99362789902125e-11 2.96778269781362e-08 20 411338 472482 1457
C17orf59 0.7495 1.06524566945154e-10 4.26929112473842e-08 17 8032376 8034115 54785
SENP2 0.7462 1.43219658355065e-10 5.43785384520582e-08 3 186786725 186831583 59343
AP1M1 0.7446 1.64789515366692e-10 5.94399012380375e-08 19 16169731 16207151 8907
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.