Kidney Renal Papillary Cell Carcinoma: 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 913.1, 2044.2, 2696, 3257, 3807, 4349, 4905.7, 5516, 6256.9, 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 75 63 63
Genes 22749 18200 17452

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
25844 YIPF3 6p21.1 0.8351 0 0
9587 MAD2L1BP 6p21.1 0.8252 0 0
9477 MED20 6p21.1 0.8229 0 0
129685 TAF8 6p21.1 0.8094 8.88178419700125e-16 1.54903776874098e-12
23197 FAF2 5q35.2 0.8031 2.44249065417534e-15 3.40788309123015e-12
55750 AGK 7q34 0.797 5.55111512312578e-15 6.45432403642073e-12
55173 MRPS10 6p21.1 0.7936 8.88178419700125e-15 8.85164439280557e-12
23070 FTSJD2 6p21.2 0.7841 2.97539770599542e-14 2.59463826264113e-11
5528 PPP2R5D 6p21.1 0.7826 3.59712259978551e-14 2.78826798373376e-11
26168 SENP3 17p13.1 0.7678 2.1138646388863e-13 1.35798977726292e-10
57798 GATAD1 7q21.2 0.7675 2.18491891246231e-13 1.35798977726292e-10
78996 C7orf49 7q33 0.7669 2.33590924381133e-13 1.35798977726292e-10
222234 FAM185A 7q22.1 0.7631 3.60600438398251e-13 1.9351056434118e-10
9025 RNF8 6p21.2 0.7617 4.20108392518159e-13 2.09341389889852e-10
23567 ZNF346 5q35.2 0.7605 4.83613149526718e-13 2.2492028402119e-10
1801 DPH1 17p13.3 0.7596 5.33351141029925e-13 2.32549295032239e-10
10548 TM9SF1 14q12 0.7548 9.02833363625177e-13 3.6557291342287e-10
57470 LRRC47 1p36.32 0.7542 9.5634611341211e-13 3.6557291342287e-10
56897 WRNIP1 6p25.2 0.7536 1.01896269200097e-12 3.6557291342287e-10
55776 SAYSD1 6p21.2 0.7534 1.04805053524615e-12 3.6557291342287e-10
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. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.