Correlation between mRNA expression and DNA methylation
Bladder Urothelial Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1FJ2DSN
Maintained by Richard Park (Boston University/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between mRNA expression and DNA methylation. Broad Institute of MIT and Harvard. doi:10.7908/C1FJ2DSN
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 = 149. Number of gene expression samples = 149. Number of methylation samples = 153.

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 = 149

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 -0.89 0 0 7 0.67
cg13101072 FAM50B 6 3849818 -0.87 0 0 5.6 0.61
cg00032205 TSPYL5 8 98290372 -0.87 0 0 8.4 0.35
cg09781936 TBX1 22 19749961 -0.86 0 0 7.2 0.61
cg22040809 HCG11 6 26522578 -0.86 0 0 7 0.52
cg06360527 SOX15 17 7491548 -0.86 0 0 7.1 0.51
cg21171625 DNALI1 1 38022607 -0.86 0 0 5.4 0.54
cg13030332 TBX3 12 115117351 -0.85 0 0 11 0.49
cg12557114 WISP3 6 112375870 -0.85 0 0 4.2 0.76
cg16785938 SLC2A9 4 10022984 -0.84 0 0 7 0.48
cg09298971 SLC44A4 6 31846249 -0.84 0 0 8 0.74
cg08036899 IFI27 14 94577218 -0.84 0 0 11 0.64
cg22718139 HMGCS2 1 120311439 -0.83 0 0 7.9 0.68
cg07353685 S100A2 1 153536278 -0.83 0 0 11 0.56
cg21145686 GPD1L 3 32149153 -0.83 0 0 9.9 0.39
cg16048383 SCNN1A 12 6483708 -0.83 0 0 9.5 0.63
cg05046097 SNCG 10 88717926 -0.83 0 0 11 0.51
cg01648237 C2orf74 2 61372066 -0.83 0 0 6 0.36
cg26511386 TMEM139 7 142982262 -0.82 0 0 6.2 0.54
cg06972565 TNFRSF21 6 47272740 -0.82 0 0 13 0.57
cg18580265 EPHX3 19 15343170 -0.82 0 0 6.7 0.43
cg06368590 TRPS1 8 116679763 -0.82 0 0 7 0.53
cg16850945 TNNC1 3 52488229 -0.82 0 0 5.1 0.55
cg21330727 RAPGEFL1 17 38336206 -0.82 0 0 11 0.42
cg26155983 GPX2 14 65410145 -0.82 0 0 10 0.61
cg15518883 SIT1 9 35650561 -0.81 0 0 4.1 0.77
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/BLCA-TP/3527686/BLCA-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/BLCA-TP/3350935/BLCA-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.

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