Glioblastoma Multiforme: Correlation between mRNA expression and DNA methylation
(primary solid tumor cohort)
Maintained by Richard Park (Boston University/Harvard Medical School)
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 = 47. Number of gene expression samples = 154. Number of methylation samples = 47.

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 = 47

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
cg12889195 LOC654433 2 113992843 -0.91 0 0 7.027 0.785235
cg01586506 SOX10 22 38379506 -0.89 0 0 8.445 0.819123
cg12889195 PAX8 2 113992843 -0.88 0 0 4.912 0.785235
cg04755771 LOC134466 5 150326521 -0.87 0 0 4.216 0.562585
cg03001832 HTATIP2 11 20385172 -0.87 0 0 8.018 0.366023
cg05127217 TTC12 11 113185802 -0.86 0 0 6.476 0.364387
cg01305625 PDLIM4 5 131593812 -0.86 0 0 8.844 0.676743
cg17739279 FAM50B 6 3849190 -0.86 0 0 7.207 0.658094
cg26776069 DEM1 1 40974239 -0.85 0 0 6.745 0.283496
cg13906823 TSTD1 1 161008824 -0.84 0 0 7.085 0.445222
cg16482344 LOC84856 10 42970987 -0.84 0 0 NA 0.624657
cg04134305 C7orf13 7 156433520 -0.84 0 0 5.234 0.494930
cg21350115 CALCRL 2 188312833 -0.84 0 0 9.948 0.355268
cg00790847 SLC2A13 12 40497575 -0.84 0 0 8.526 0.621961
cg00654888 EN1 2 119603133 -0.83 0 0 NA 0.352083
cg15013496 SALL3 18 76745056 -0.83 0 0 8.162 0.153912
cg24075113 TRIP6 7 100465289 -0.83 0 0 10.690 0.212709
cg21195256 C14orf23 14 29244278 -0.83 0 0 5.719 0.166034
cg11218091 FAM24B 10 124638976 -0.82 0 0 NA 0.432734
cg18675097 NKAPL 6 28227127 -0.82 1.4e-12 2.5e-11 3.290 0.714284
cg20258486 LOC154822 7 158800888 -0.82 0 0 6.343 0.492813
cg26093711 VRK2 2 58273654 -0.82 0 0 6.614 0.447553
cg24881834 ME1 6 84140997 -0.82 0 0 7.278 0.488063
cg06198069 NNAT 20 36151184 -0.82 0 0 9.156 0.753354
cg15147690 FABP5 8 82192931 -0.81 0 0 6.758 0.274943
cg18809076 EGFR 7 55177623 -0.81 0 0 11.639 0.388308
Methods & Data
Input

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

  • methylation file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/GBM-TP/2541714/0.GDAC_MethylationPreprocess.Finished/GBM-TP.meth.for_correlation.filtered_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/GBM-TP/2540122/0.mRNAseq_preprocessor.Finished/GBM-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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.