Thyroid Adenocarcinoma: 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 524.2, 1159.4, 2126.6, 2751, 3216, 3650.2, 4146.4, 4717.6, 5479.8, 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 228 78 78
Genes 22749 17936 17193

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
5728 PTEN 10q23.31 0.8706 0 0
51493 C22orf28 22q12.3 0.8056 0 0
51386 EIF3L 22q13.1 0.7878 0 0
54471 SMCR7L 22q13.1 0.785 0 0
10454 TAB1 22q13.1 0.7796 0 0
24144 TFIP11 22q12.1 0.7726 0 0
83698 CALN1 7q11.22 0.7564 1.01862962509358e-11 3.30584977165589e-09
6598 SMARCB1 22q11.23 0.7547 1.33226762955019e-15 1.89828307635882e-12
2547 XRCC6 22q13.2 0.7429 6.88338275267597e-15 7.52985620288997e-12
55328 RNLS 10q23.31 0.7423 7.54951656745106e-15 7.52985620288997e-12
158 ADSL 22q13.1 0.7421 7.54951656745106e-15 7.52985620288997e-12
613 BCR 22q11.23 0.7365 1.53210777398272e-14 1.29188709363308e-11
25814 ATXN10 22q13.31 0.7364 1.55431223447522e-14 1.29188709363308e-11
6767 ST13 22q13.2 0.7353 1.77635683940025e-14 1.36286990097556e-11
9701 PPP6R2 22q13.33 0.7275 4.57411886145564e-14 3.25871928108264e-11
83606 C22orf13 22q11.23 0.7208 9.9920072216264e-14 6.64399076725586e-11
25771 TBC1D22A 22q13.31 0.7144 2.07833750209829e-13 1.26481898309982e-10
84896 ATAD1 10q23.31 0.7137 2.24709140184132e-13 1.26481898309982e-10
23760 PITPNB 22q12.1 0.7135 2.28261853862932e-13 1.26481898309982e-10
9562 MINPP1 10q23.2 0.7125 2.56905607898261e-13 1.34861356451141e-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.