Thyroid Adenocarcinoma: Correlation between mRNA expression and DNA methylation
(tall-cell 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 = 29. Number of gene expression samples = 29. Number of methylation samples = 29.

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 = 29

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
--- | --- | --- | --- | --- | --- | --- | --- | ---
cg11763394 | LOC654433 | 2 | 113992921 | -0.95 | 7.2e-08 | 0.000037 | 3.895684 | 0.908139
cg02384546 | ZNF750 | 17 | 80798013 | -0.89 | 5.5e-07 | 0.000037 | 7.224381 | 0.651826
cg26310000 | KLK11 | 19 | 51529846 | -0.88 | 9.2e-07 | 0.000037 | NA | 0.744458
cg24040502 | NLRP2 | 19 | 55477810 | -0.88 | 6.7e-07 | 0.000037 | 7.478866 | 0.654361
cg09079252 | FAM90A1 | 12 | 8380050 | -0.88 | 6.8e-07 | 0.000037 | 3.271031 | 0.729408
cg05021589 | LY86 | 6 | 6588931 | -0.88 | 7e-07 | 0.000037 | 6.649432 | 0.787712
cg07067982 | SLC43A3 | 11 | 57194370 | -0.87 | 7.6e-07 | 0.000037 | 10.701027 | 0.343754
cg11615029 | COL1A1 | 17 | 48263189 | -0.87 | 7.9e-07 | 0.000037 | 14.505474 | 0.949512
cg14668747 | ALDOC | 17 | 26904053 | -0.86 | 8.3e-07 | 0.000037 | 6.192839 | 0.314009
cg19850333 | CCRL2 | 3 | 46448579 | -0.86 | 8.5e-07 | 0.000037 | 5.245875 | 0.609666
cg07775813 | SPESP1 | 15 | 69223368 | -0.86 | 8.7e-07 | 0.000037 | 3.999663 | 0.806048
cg23352695 | EVI2A | 17 | 29648811 | -0.86 | 8.7e-07 | 0.000037 | 7.154004 | 0.832338
cg08686960 | COX7A1 | 19 | 36642720 | -0.86 | 8.9e-07 | 0.000037 | 7.105839 | 0.656193
cg26648103 | SYT12 | 11 | 66791718 | -0.85 | 9.4e-07 | 0.000037 | 10.949072 | 0.304767
cg24459792 | LAPTM5 | 1 | 31230846 | -0.85 | 9.6e-07 | 0.000037 | 11.325048 | 0.797817
cg08075204 | BIN2 | 12 | 51718112 | -0.85 | 9.8e-07 | 0.000037 | 6.790268 | 0.897736
cg08373528 | PRPH2 | 6 | 42672105 | -0.85 | 9.9e-07 | 0.000037 | 4.175153 | 0.542698
cg25451120 | ABI3 | 17 | 47287444 | -0.85 | 1e-06 | 0.000037 | 7.669092 | 0.680050
cg27398499 | TACSTD2 | 1 | 59043873 | -0.84 | 1.1e-06 | 0.000037 | 13.526185 | 0.262037
cg00762623 | C7orf40 | 7 | 45026020 | -0.84 | 1.1e-06 | 0.000037 | 6.388065 | 0.230805
cg03020208 | AQP5 | 12 | 50354962 | -0.84 | 1.1e-06 | 0.000037 | 6.626074 | 0.470917
cg18512948 | REC8 | 14 | 24641706 | -0.84 | 1.1e-06 | 0.000037 | 6.250053 | 0.624066
cg27370558 | CACNA1A | 19 | 13397515 | -0.83 | 1.4e-06 | 0.000037 | NA | 0.937255
cg05138203 | ITGBL1 | 13 | 102104707 | -0.83 | 1.2e-06 | 0.000037 | 8.307719 | 0.901491
cg18157738 | IGFN1 | 1 | 201161205 | -0.83 | 1.5e-06 | 0.000037 | NA | 0.709252
cg10950111 | GJC2 | 1 | 228337379 | -0.83 | 1.2e-06 | 0.000037 | 4.966114 | 0.778735

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-tall-cell/2851561/0.GDAC_MethylationPreprocess.Finished/THCA-tall-cell.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-tall-cell/2851208/0.mRNAseq_preprocessor.Finished/THCA-tall-cell.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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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