Rectum Adenocarcinoma: Correlations between copy number and mRNA expression<BR>(primary solid tumor cohort)

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 -0.06358, 0.0159, 0.0839, 0.1504, 0.2189, 0.28782, 0.36034, 0.4398, 0.5357, 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	162	69	68
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
CNOT7	0.8524	0	0	8	17131108	17148758	29883
APTX	0.8465	0	0	9	32962608	32991626	54840
DSTN	0.8338	0	0	20	17498599	17536652	11034
VPS37A	0.8271	0	0	8	17148851	17197418	137492
PSMF1	0.8221	0	0	20	1041939	1095971	9491
TSPAN14	0.817	0	0	10	82204047	82269366	81619
PINX1	0.816	0	0	8	10659883	10734796	54984
DYNLRB1	0.8114	0	0	20	32567865	32592423	83658
CDC16	0.8089	0	0	13	114018476	114056252	8881
GTF2E2	0.8062	0	0	8	30555573	30635274	2961
TMEM11	0.8041	0	0	17	21041855	21058297	8834
DDX20	0.803	2.22044604925031e-16	1.09728331689964e-13	1	112099777	112111722	11218
TMEM93	0.7982	4.44089209850063e-16	1.75565330703942e-13	17	3518839	3519711	83460
CUL4A	0.7961	4.44089209850063e-16	1.75565330703942e-13	13	112911087	112967393	8451
C20orf77	0.7949	4.44089209850063e-16	1.75565330703942e-13	20	36095467	36154632	58490
LOC400506	0.7926	8.88178419700125e-16	3.09821171830485e-13	16	19625733	19633856	400506
C20orf72	0.791	8.88178419700125e-16	3.09821171830485e-13	20	17897762	17919761	92667
CTNNBL1	0.7891	1.33226762955019e-15	4.15812625351441e-13	20	35755848	35933934	56259
ZNF133	0.7886	1.33226762955019e-15	4.15812625351441e-13	20	18217157	18245640	7692
MRPL51	0.7848	2.22044604925031e-15	6.58369990139781e-13	12	6471577	6472718	51258

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.