Correlations between APOBEC_MutLoad_MinEstimate and mRNAseq expression
Lung Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by Hailei Zhang (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlations between APOBEC_MutLoad_MinEstimate and mRNAseq expression. Broad Institute of MIT and Harvard. doi:10.7908/C1PK0FK4

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 -0.0901, -0.0555, -0.0299, -0.0076, 0.0129, 0.0343, 0.0565, 0.0819, 0.1179, 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 178 501 178

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
TSPYL6|388951 0.5772 3.16434416447464e-08 0.000585846678610835
C11orf86|254439 0.4769 2.61463648874027e-05 0.0691533999321963
SLC10A1|6554 0.4138 2.28025533215437e-05 0.0691533999321963
FAM75C1|441452 0.4086 0.000885177113341795 0.372458388100227
ATP4B|496 0.4056 0.000802346794357867 0.372378037004076
ALPP|250 0.3523 7.41261393644166e-06 0.0410068770173548
OLFM4|10562 0.3471 4.32222384172398e-06 0.0400108261028389
C11orf85|283129 0.3425 0.00643617278344699 0.57937921309843
CYP4F8|11283 0.3382 0.0152177543398606 0.656740102210208
CGA|1081 0.3333 0.00236277267216645 0.492232359473852
C20orf141|128653 0.3273 0.00344135298672987 0.544557343558264
INHA|3623 0.3271 8.85964718966292e-06 0.0410068770173548
AMAC1|146861 0.3263 0.00849798649148492 0.591472638734405
TRIM17|51127 0.3156 1.77367862410627e-05 0.0656757720934069
C8G|733 0.313 3.8124254579941e-05 0.0882290561616283
LCE5A|254910 0.3036 0.0100476233776328 0.614590738754272
OR1F1|4992 0.3022 0.00291919812566244 0.510456062793209
CNTD2|79935 0.2988 6.85069099315427e-05 0.126833693047258
THRSP|7069 0.2988 0.00788721539538573 0.591472638734405
GPR78|27201 0.2968 0.0236579483031365 0.704713159984946
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.