Figure 3: Distribution of β values among genomic features and BM type specific clustering. | Scientific Data

Figure 3: Distribution of β values among genomic features and BM type specific clustering.

From: Brain metastasis DNA methylomes, a novel resource for the identification of biological and clinical features

Figure 3

(a) The distribution of DNAm levels in low-CpG density regions (i.e. open sea, CGI shelf, and CGI shore) with respect to high-CpG density CGIs. (b) The distribution of DNAm levels for CpG sites with respect to gene compartments in the promoter regions, 5’UTRs, the 1st exon, gene body, and intergenic regions (IGRs). Box colors indicate BM subtype, with green boxes representing breast cancer brain metastases (BCBM), orange boxes representing lung cancer brain metastases (LCBM), and purple boxes representing melanoma brain metastases (MBM). (c) t-SNE analysis reveals BM subtype specific clustering of samples. The top 2,500 most variable CpG sites were used for the analysis with the first two dimensions shown. Each of the three BM subtypes is confined to a cluster, with MBMs depicted in purple, BCBMs depicted in green, and LCBMs depicted in orange. No samples were found to fall outside of a BM subtype specific cluster

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