Bladder Urothelial Carcinoma: Correlations between copy number and mRNAseq expression

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 945, 2192, 3002, 3739, 4467, 5200, 5935, 6726, 7553, 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	56	32	32
Genes	22749	18086	17321

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
81037	CLPTM1L	5p15.33	0.9407	1.33226762955019e-15	6.6258052258649e-12
329	BIRC2	11q22.2	0.9395	1.77635683940025e-15	6.6258052258649e-12
9785	DHX38	16q22.2	0.937	3.10862446895044e-15	7.73010609684239e-12
10948	STARD3	17q12	0.9306	1.24344978758018e-14	2.31903182905272e-11
51250	C6orf203	6q21	0.9294	1.59872115546023e-14	2.38528988131136e-11
336	APOA2	1q23.3	0.9273	3.96594799518812e-05	0.000175688516699132
64789	DEM1	1p34.2	0.9266	2.79776202205539e-14	3.2655754327477e-11
22887	FOXJ3	1p34.2	0.9262	3.06421554796543e-14	3.2655754327477e-11
8089	YEATS4	12q15	0.9251	3.75255382323303e-14	3.4992533849099e-11
5908	RAP1B	12q15	0.918	1.38333788868295e-13	1.14663240436495e-10
84259	DCUN1D5	11q22.3	0.9155	2.1449508835758e-13	1.60013196204637e-10
5894	RAF1	3p25.2	0.9147	2.45137243837235e-13	1.66247476576247e-10
8834	TMEM11	17p11.2	0.914	2.76667577736589e-13	1.71994860654743e-10
3845	KRAS	12p12.1	0.9133	3.09530179265494e-13	1.77622547785686e-10
9861	PSMD6	3p14.1	0.9121	3.81916720471054e-13	2.03506874794422e-10
7862	BRPF1	3p25.3	0.9105	4.90274487674469e-13	2.43829632311828e-10
5082	PDCL	9q33.2	0.9089	6.3948846218409e-13	2.98161235163921e-10
8994	LIMD1	3p21.31	0.9065	9.2637009174723e-13	4.06512638269241e-10
55508	SLC35E3	12q15	0.9056	1.06314956838105e-12	4.40616047520016e-10
54901	CDKAL1	6p22.3	0.9047	1.21058718605127e-12	4.75314343308098e-10

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.