Thyroid Adenocarcinoma: Correlation between mRNA expression and DNA methylation
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 = 158. Number of gene expression samples = 158. Number of methylation samples = 158.

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 = 158

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
cg06787669 MYO1G 7 44985314 -0.9 0 0 8.110 0.578923
cg08480068 SPN 16 29582460 -0.88 0 0 6.874 0.900702
cg25571414 SLC34A2 4 25268670 -0.87 0 0 14.120 0.600533
cg21163717 DOK2 8 21825849 -0.87 0 0 6.134 0.817052
cg11763394 LOC654433 2 113709392 -0.87 0 0 4.142 0.905671
cg24749672 BIN2 12 50004375 -0.87 0 0 6.236 0.881680
cg16983159 TMEM173 5 138842625 -0.86 0 0 10.060 0.380875
cg10397389 DAPP1 4 100957034 -0.86 0 0 4.724 0.807421
cg07150145 PDZK1IP1 1 47428724 -0.85 0 0 NA 0.366166
cg09897970 C16orf54 16 29664845 -0.85 0 0 4.475 0.849651
cg27398499 TACSTD2 1 58816461 -0.84 0 0 11.731 0.400328
cg18738906 SCNN1A 12 6354000 -0.84 0 0 11.383 0.709211
cg00041401 PTPN22 1 114215931 -0.84 0 0 4.470 0.789674
cg26648103 SYT12 11 66548294 -0.84 0 0 8.764 0.403094
cg11787522 STRA6 15 72282162 -0.83 0 0 7.464 0.462910
cg15761609 FAM20A 17 64109662 -0.83 0 0 9.765 0.331443
cg22502856 LAMB3 1 207892301 -0.83 0 0 10.501 0.740206
cg17418085 LAPTM5 1 31001709 -0.83 0 0 10.748 0.773497
cg26230275 S100A10 1 150231907 -0.83 0 0 10.717 0.539312
cg18157738 IGFN1 1 199427828 -0.83 0 0 NA 0.780175
cg25651476 NLRP2 19 60168529 -0.83 0 0 NA 0.566893
cg07675031 SPI1 11 47356469 -0.83 0 0 7.803 0.906920
cg17290213 EHBP1L1 11 65100931 -0.82 0 0 9.406 0.530744
cg06799735 AHNAK2 14 104508186 -0.82 0 0 10.129 0.616016
cg10156217 ARF6 14 49432104 -0.82 0 0 11.394 0.398994
cg11619602 ARNTL 11 13317283 -0.82 0 0 9.955 0.583420
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/THCA/1841599/0.GDAC_MethylationPreprocess.Finished/THCA.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/THCA/1768868/0.mRNAseq_preprocessor.Finished/THCA.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.