DNA methylation levels determined using Illumina's Infinium 450 K array were downloaded as β-values. We chose a cut-off of 10% to distinguish between methylated and unmethylated loci, as previously published.(17 (link)) All promoter methylation probes located 1 kb upstream of the transcriptional start site were considered for each gene. For genes with multiple promoter methylation probes, analyses were carried out for probes least correlated with mRNA expression to minimize false positive results. mRNA expression was downloaded as RNA-Seq by Expectation Maximization values(18 (link)) from the cBioPortal freeware (http://www.cbioportal.org/public-portal .(19 (link),20 (link)) Only samples with matched DNA methylation and mRNA expression data were included in this analysis (n = 173).
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Promoter Methylation and mRNA Expression
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Other organizations : Centenary Institute, University of Sydney, Royal Prince Alfred Hospital
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Variable analysis
independent variables
- DNA methylation levels determined using Illumina's Infinium 450 K array
- MRNA expression downloaded as RNA-Seq by Expectation Maximization values
- Samples with matched DNA methylation and mRNA expression data (n = 173)
- No positive or negative controls were explicitly mentioned in the input.
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