Project_Genes: Phase 3

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Differential Methylation analysis_regulatory regions:

• Annotate relevant CpGs by regulatory region
• Separate hyper/hypomethylated genes
• Gene ranking, now with additional regulatory region information

(Decide which genes are actually interesting for KIRC.

Good candidate genes should have:

• multiple significant CpGs
• large methylation difference between tumor and normal
• consistent direction across CpGs
• clear separation in boxplots or heatmaps
• known or plausible relevance to KIRC/cancer biology

For top genes, make visualizations:

• boxplots of methylation per gene or per CpG
• heatmap of CpGs belonging to top genes
• tumor vs normal methylation plots

For each top gene, ask:

• Is it hypermethylated or hypomethylated in tumor?
• Is the pattern consistent across samples?
• Is the change driven by one CpG or several CpGs?
• Does tumor clearly separate from normal?)