Correlations between APOBEC_MutLoad_MinEstimate and mRNAseq expression
Breast Invasive Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
Maintained by Hailei Zhang (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlations between APOBEC_MutLoad_MinEstimate and mRNAseq expression. Broad Institute of MIT and Harvard. doi:10.7908/C10R9NKJ

This pipeline attempts to calculate the pearson correlation between APOBEC_MutLoad_MinEstimate and mRnaseq data of each gene across samples to determine if the APOBEC_MutLoad_MinEstimate also result in differential expressions.


The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.0567, -0.0398, -0.026, -0.0142, -0.0036, 0.007, 0.0182, 0.0315, 0.0499, respectively.

Correlation results

Number of 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 genes ordered by the value of correlation coefficients.

Table 1.  Counts of mRNAseq and number of samples in APOBEC_MutLoad_MinEstimate and expression data sets and common to both

Category APOBEC_MutLoad_MinEstimate Expression Common
Sample 978 1093 974

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 genes ranked by correlation coefficients

geneID cor p-value q-value
HFE2|148738 0.3017 4.92876051083613e-09 4.50883011531289e-05
CACNA1S|779 0.266 3.46300125286803e-06 0.00289035671378529
ABRA|137735 0.2251 3.20085347116361e-07 0.000532389228258268
TBX10|347853 0.1932 0.000293478731580699 0.0431638279629016
PROKR1|10887 0.1926 2.19678084611985e-05 0.00803846047212176
OR1Q1|158131 0.1874 0.000533310389485564 0.0627924417907852
CHRNA4|1137 0.1835 0.000168260230674289 0.0292741389024907
SUSD2|56241 0.1796 1.65089473203039e-08 7.55119250430702e-05
CDH10|1008 0.177 0.00027573679993953 0.0413514794401118
SNX11|29916 0.1727 5.80909835790067e-08 0.000151833233651644
ASB5|140458 0.172 0.00160128154558414 0.106534716938209
OVCH1|341350 0.1719 0.00156694912835098 0.106487689515663
LOC400891|400891 0.1701 0.00114086424729853 0.091549352055149
FBXO40|51725 0.167 0.000410011890184858 0.0531349807878518
KCNT1|57582 0.1618 5.88433384707265e-06 0.00371240593331177
MYL2|4633 0.1593 0.00164242111564783 0.108482804086255
TMC1|117531 0.159 2.89909036019775e-05 0.00959964512502387
SLC10A1|6554 0.1579 0.00136000789368351 0.099134280569058
TEX11|56159 0.1579 3.38379499642549e-06 0.00289035671378529
SEPX1|51734 0.1563 9.474744027127e-07 0.00131686632153752
Methods & Data

Gene level (TCGA Level III) mRNAseq expression data and APOBEC_MutLoad_MinEstimate derived by Mutation_APOBEC pipeline were used to do this analysis. Pearson correlation coefficients were calculated for APOBEC_MutLoad_MinEstimate and each gene across all the samples that were common.

Correlation across sample

Pearson correlation with pairwise.complete.obs was used to do this analysis.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.