Correlation between mRNA expression and DNA methylation
Thymoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by Richard Park (Boston University/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between mRNA expression and DNA methylation. Broad Institute of MIT and Harvard. doi:10.7908/C1FX78DR
Overview
Introduction

The role of general epigenetic mechanisms in carcinogenesis and tumor aggressiveness is well documented: CpG island hyper-methylation silences tumor suppressor genes, whereas hypo-methylation promotes the transcriptional activation of oncogenes and induces chromosomal instability. This pipeline calculates and identifies correlations between DNA methylation and gene expression profiles using the available array technologies.

Summary

The top 25 correlated methylation probes per gene are displayed. Total number of matched samples = 116. Number of gene expression samples = 116. Number of methylation samples = 124.

Results
Correlation Histogram

Figure 1.  Histogram of methylation correlation values. n is the number of matched samples between Level 3 CpG site methylation and Level 3 gene expression arrays. Number of Matched Samples = 116

Qvalue Summary Plots

Figure 2.  Plot 1. The estimated pi_0 versus the tuning parameter lambda. Plot 2. The q-values versus the p-values. Plot 3. The number of significant tests versus each q-value cutoff. Plot 4. The number of expected false positives versus the number of significant tests.The first is a plot of the estimate of pi_0 versus its tuning parameter lambda. In most cases, as lambda gets larger, the bias of the estimate decreases, yet the variance increases. Comparing your estimate of pi_0 to this plot allows one to guage its quality. The remaining three plots show how many tests are significant, as well as how many false positives to expect for each q-value cut-off.

Negative Correlation between Methylation and Gene Expression

Table 1.  Get Full Table Top 25 most negatively correlated methylation probes. Correlation Coefficient: See Methods & Data below. Pval and Qval: P- and Q-values of the correlation coefficient. Expression Mean: mean detection level of gene expression probes. Methylation Mean: mean detection level of CpG methylation probes.

Meth_Probe Gene Chrom Position Corr_Coeff Pval Qval Expr_Mean Meth_Mean
cg09554443 CD247 1 167487762 -0.95 0 0 11 0.43
cg26163153 RHOH 4 40197912 -0.94 0 0 9.9 0.45
cg05959508 TRAF3IP3 1 209929512 -0.94 0 0 10 0.36
cg00147751 PVRIG 7 99818709 -0.93 0 0 10 0.36
cg00903584 PTPN7 1 202128682 -0.93 0 0 11 0.43
cg08777095 CD8B 2 87052406 -0.93 0 0 12 0.44
cg14644204 PITPNM2 12 123518833 -0.93 0 0 11 0.45
cg03016153 CD2 1 117296954 -0.93 0 0 11 0.52
cg25939861 CD8A 2 87020937 -0.93 0 0 12 0.62
cg27354586 CD3E 11 118175172 -0.93 0 0 12 0.48
cg10590292 BIN2 12 51717674 -0.92 0 0 9.7 0.5
cg10673833 MYO1G 7 45018849 -0.92 0 0 10 0.5
cg00302479 PSD4 2 113931538 -0.92 0 0 11 0.37
cg09354050 UBASH3A 21 43824262 -0.92 0 0 8.6 0.39
cg24147838 LAIR1 19 54876664 -0.92 0 0 11 0.46
cg10361659 RNASEH2B 13 51482542 -0.91 0 0 11 0.54
cg01143547 CCND3 6 41903527 -0.91 0 0 13 0.55
cg25765104 RCSD1 1 167601275 -0.91 0 0 11 0.43
cg12710152 LCK 1 32716773 -0.91 0 0 12 0.39
cg12005186 FERMT3 11 63973952 -0.91 0 0 11 0.33
cg24674703 CD5 11 60869960 -0.91 0 0 9.9 0.43
cg21376733 NCKAP1L 12 54891636 -0.91 0 0 10 0.41
cg21773162 ZAP70 2 98330087 -0.91 0 0 11 0.37
cg13750061 CD3G 11 118214845 -0.91 0 0 8.7 0.52
cg24841244 CD3D 11 118213330 -0.9 0 0 12 0.49
cg12623364 LEF1 4 109038130 -0.9 0 0 12 0.38
Methods & Data
Input

Methylation Array Platforms: Illumina Infinium HumanMethylation27, Illumina Infinium HumanMethylation450, Illumina DNA Methylation OMA002, Illumina DNA Methylation OMA003

  • methylation file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/THYM-TP/11493998/THYM-TP.meth.by_min_expr_corr.data.txt

Gene Expression Platforms: Agilent 244K Gene Expression G4502A-07-1, Agilent 244K Gene Expression G4502A-07-2, Agilent 244K Gene Expression G4502A-07-3, Affymetrix Human Exon 1.0 ST Array, Affymetrix HT Human Genome U133 Array

  • gene expression file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THYM-TP/11493749/THYM-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

Correlation Coefficient

Level 3 methylation and gene expression arrays were paired on the basis of Entrez Gene ID concordance. The association between CpG site methylation and the level of expression of the corresponding genes was determined by calculating a correlation measure between the two platforms.

  • correlation measure = Spearman

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.