Skin Cutaneous Melanoma: 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 = 247. Number of gene expression samples = 247. Number of methylation samples = 247.

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 = 247

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
--- | --- | --- | --- | --- | --- | --- | --- | ---
cg11578532 | TSTD1 | 1 | 161008127 | -0.89 | 0 | 0 | 5.100 | 0.673170
cg21171625 | DNALI1 | 1 | 38022607 | -0.89 | 0 | 0 | 5.299 | 0.561969
cg15518883 | SIT1 | 9 | 35650561 | -0.89 | 0 | 0 | NA | 0.746751
cg02685484 | PTPRCAP | 11 | 67203360 | -0.88 | 0 | 0 | 7.460 | 0.797371
cg03669949 | DDX43 | 6 | 74104426 | -0.88 | 2.9e-66 | 1.4e-66 | NA | 0.783779
cg20317872 | DENND2D | 1 | 111743202 | -0.88 | 0 | 0 | 7.644 | 0.685506
cg05462570 | NAALADL1 | 11 | 64814948 | -0.88 | 0 | 0 | 5.192 | 0.402579
cg16068833 | CD52 | 1 | 26644515 | -0.87 | 0 | 0 | 7.716 | 0.717691
cg07786657 | CD247 | 1 | 167487633 | -0.87 | 0 | 0 | 5.962 | 0.790606
cg01072786 | GLB1L | 2 | 220107847 | -0.85 | 0 | 0 | 8.908 | 0.573836
cg21249754 | PTPN6 | 12 | 7060206 | -0.85 | 0 | 0 | 8.866 | 0.716473
cg05564251 | SP140 | 2 | 231090640 | -0.85 | 0 | 0 | 6.107 | 0.718818
cg00903584 | PTPN7 | 1 | 202128682 | -0.84 | 0 | 0 | 7.526 | 0.668815
cg11550547 | KCTD14 | 11 | 77734490 | -0.84 | 0 | 0 | NA | 0.661828
cg07682037 | FERMT3 | 11 | 63974153 | -0.84 | 0 | 0 | 9.590 | 0.500522
cg00032205 | TSPYL5 | 8 | 98290372 | -0.84 | 0 | 0 | 7.180 | 0.563246
cg25671438 | ACAP1 | 17 | 7240223 | -0.84 | 0 | 0 | 6.575 | 0.584779
cg12947833 | HSPB2 | 11 | 111783499 | -0.84 | 0 | 0 | 7.256 | 0.322449
cg16462073 | LAT | 16 | 28995843 | -0.84 | 0 | 0 | 7.294 | 0.797119
cg10402417 | TBC1D10C | 11 | 67171476 | -0.84 | 0 | 0 | 6.272 | 0.608054
cg05656364 | VAMP8 | 2 | 85804732 | -0.84 | 0 | 0 | 9.358 | 0.457456
cg07994485 | FAM178B | 2 | 97652440 | -0.83 | 0 | 0 | NA | 0.665726
cg01305625 | PDLIM4 | 5 | 131593812 | -0.83 | 0 | 0 | 8.013 | 0.680818
cg04253799 | LOC100128675 | 19 | 35597062 | -0.83 | 0 | 0 | NA | 0.642037
cg08075204 | BIN2 | 12 | 51718112 | -0.83 | 0 | 0 | 7.033 | 0.776919
cg24674703 | CD5 | 11 | 60869960 | -0.83 | 0 | 0 | 6.303 | 0.763789

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/SKCM/2009134/0.GDAC_MethylationPreprocess.Finished/SKCM.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/SKCM/2008935/0.mRNAseq_preprocessor.Finished/SKCM.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)

Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle