Bladder Urothelial Carinoma: Correlations between copy number and mRNAseq expression
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)

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.


The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 953.1, 2073.2, 2793, 3464, 4157.5, 4853, 5559, 6276.8, 7075.9, respectively.

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 56 55
Genes 22749 19115 18262

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
55508 SLC35E3 12q15 0.9003 0 0
51250 C6orf203 6q21 0.8992 0 0
84299 MIEN1 17q12 0.8813 0 0
4802 NFYC 1p34.2 0.875 0 0
8089 YEATS4 12q15 0.8743 0 0
441061 MARCH11 5p15.1 0.8742 4.47575389039834e-06 1.30983908226919e-05
10818 FRS2 12q15 0.872 0 0
10450 PPIE 1p34.2 0.8706 0 0
10948 STARD3 17q12 0.8706 0 0
91782 CHMP7 8p21.3 0.8677 0 0
5709 PSMD3 17q21.1 0.8633 0 0
220064 ORAOV1 11q13.3 0.8586 0 0
51759 C9orf78 9q34.11 0.8583 0 0
79648 MCPH1 8p23.1 0.8536 0 0
329 BIRC2 11q22.2 0.8517 2.22044604925031e-16 1.02671299558178e-13
8500 PPFIA1 11q13.3 0.8496 2.22044604925031e-16 1.02671299558178e-13
3845 KRAS 12p12.1 0.8481 4.44089209850063e-16 1.71118832596964e-13
23185 LARP4B 10p15.3 0.8469 4.44089209850063e-16 1.71118832596964e-13
4507 MTAP 9p21.3 0.8464 4.44089209850063e-16 1.71118832596964e-13
55246 CCDC25 8p21.1 0.8435 6.66133814775094e-16 2.43168867374633e-13
Methods & Data

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. Location of data archives could not be determined.

  • Maintainer = TCGA GDAC Team