We downloaded precomputed genome-wide methylation data for 43 GSCs from Gene Expression Omnibus (GSE119774, RRID:SCR_005012; ref. 29 (link)). These methylation data were generated using the Illumina Infinium Epic Methylation Array. In this assay, DNA methylation levels at CpG sites are represented by β, which is the ratio of the methylated (C) to unmethylated (T) signal. We annotated the CpG probe positions based on GENCODE (v28, RRID:SCR_014966) genes and computed the mean β values for promoter regions (i.e., 1 kb upstream to 500 bp downstream of annotated transcription start sites; βpromoter). To discover ASE genes that may be dysregulated by aberrant DNA methylation, we computed Spearman rank correlation between βpromoter and normalized gene expression. We corrected correlation P values for multiple testing using the Benjamini–Hochberg procedure. For this analysis, we only considered genes with ≥ 3 CpG probes mapping to their promoter regions.
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Genome-wide Methylation Analysis of Glioma Stem Cells
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Corresponding Organization : University of Pittsburgh
Other organizations : Case Western Reserve University, Cleveland Clinic Lerner College of Medicine, Columbia University Irving Medical Center, University of Montana, Center for Discovery
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Variable analysis
independent variables
- Precomputed genome-wide methylation data for 43 GSCs
- Mean β values for promoter regions (i.e., 1 kb upstream to 500 bp downstream of annotated transcription start sites; βpromoter)
- Spearman rank correlation between βpromoter and normalized gene expression
- Kept constant to ensure valid results: Not explicitly mentioned
- Positive controls: Not explicitly mentioned
- Negative controls: Not explicitly mentioned
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