Kidney Renal Clear Cell Carcinoma: 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 probe(s) per gene are displayed. Total number of matched samples = 71 Number of gene expression samples = 221 Number of methylation samples = 72

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 = 71

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 probe(s) per gene. Correlation Coefficient: See Methods & Data below. Expression Mean and Expression Variance: median and variance of gene expression levels of gene expression probes associated with the gene. Methylation Mean and Methylation Variance: median and variance of methylation levels of CpG methylation probes associated with the gene.

Meth_Probe | Gene | Chrom | Position | Corr_Spearman | Pval_Spearman | Qval | Expr_Mean | Meth_Mean
--- | --- | --- | --- | --- | --- | --- | --- | ---
cg05798712 | FABP7 | 6 | 123142606 | -0.86 | 0 | 0 | 1.757e+00 | 0.666331
cg03054529 | SCRN1 | 7 | 29996463 | -0.75 | 0 | 0 | -1.220e+00 | 0.630337
cg18384097 | PTPN7 | 1 | 200396189 | -0.74 | 0 | 0 | -4.102e-01 | 0.801900
cg17188169 | DDX43 | 6 | 74161109 | -0.74 | 0 | 0 | -1.447e+00 | 0.817546
cg16983159 | TMEM173 | 5 | 138842625 | -0.73 | 0 | 0 | 1.558e+00 | 0.453570
cg08124399 | DDX43 | 6 | 74161589 | -0.73 | 0 | 0 | -1.447e+00 | 0.797172
cg10604646 | RGS5 | 1 | 161439273 | -0.73 | 0 | 0 | 4.977e+00 | 0.763708
cg04915566 | RUNX1 | 21 | 35343342 | -0.72 | 0 | 0 | -1.550e+00 | 0.582120
cg17439694 | CP | 3 | 150422213 | -0.72 | 0 | 0 | -4.913e-01 | 0.661399
cg20082641 | PAQR5 | 15 | 67377309 | -0.72 | 0 | 0 | 6.026e-01 | 0.505592
cg15645309 | BATF | 14 | 75058500 | -0.7 | 0 | 0 | -8.672e-02 | 0.491801
cg24892510 | ZNF415 | 19 | 58328121 | -0.7 | 0 | 0 | 5.328e-01 | 0.093802
cg03934354 | C1QTNF3 | 5 | 34078897 | -0.7 | 0 | 0 | 4.399e-01 | 0.842751
cg21820890 | PLA2G12B | 10 | 74384381 | -0.69 | 0 | 0 | 6.822e-01 | 0.717275
cg11618577 | KRTCAP3 | 2 | 27519047 | -0.69 | 0 | 0 | 7.627e-01 | 0.574675
cg20899321 | LRRC32 | 11 | 76058253 | -0.69 | 0 | 0 | 3.314e+00 | 0.816653
cg19786920 | NSUN7 | 4 | 40446527 | -0.69 | 0 | 0 | 2.017e-01 | 0.136975
cg15518883 | SIT1 | 9 | 35640561 | -0.69 | 0 | 0 | 8.073e-02 | 0.828954
cg24315815 | PLSCR4 | 3 | 147452269 | -0.68 | 0 | 0 | 2.644e+00 | 0.484081
cg07054095 | ZNF549 | 19 | 62730668 | -0.68 | 0 | 0 | -1.021e-01 | 0.090262
cg17356733 | IFNGR2 | 21 | 33696497 | -0.67 | 0 | 0 | 1.087e+00 | 0.751820
cg14721213 | FMO2 | 1 | 169421236 | -0.67 | 0 | 0 | 2.998e+00 | 0.426099
cg15046675 | CD37 | 19 | 54530589 | -0.67 | 0 | 0 | 1.213e+00 | 0.766861
cg24674703 | CD5 | 11 | 60626536 | -0.67 | 0 | 0 | -2.850e-01 | 0.847470
cg22740835 | DDR2 | 1 | 160869183 | -0.67 | 0 | 0 | -9.428e-01 | 0.832134
cg10636246 | AIM2 | 1 | 157313597 | -0.66 | 0 | 0 | 1.413e+00 | 0.597292

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_MergeDataFilesPipeline/KIRC/1269656/2.GDAC_MergeDataFiles.Finished/KIRC.methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.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/GDAC_mRNA_Preprocess_Median/KIRC/1270975/0.GDAC_mRNA_Preprocess_Median.Finished/KIRC.medianexp.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)

Meta

- Maintainer = Richard Park

Copyright © 2011 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
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