Figure 2.

MSA reveals tissue-specific methylation biology and tissue compositions

(A) t-SNE plot showing unsupervised clustering of MSA-profiled bulk tissues and sorted immune cells.

(B) Heatmap of cell-type proportion estimated by methylation-based deconvolution; columns are MSA-profiled tissues, and rows are reference cell types.

(C) Heatmaps of tissue-specific methylations (rows) across samples (columns). The bottom annotation bar indicates discriminated tissue; the left bars annotate hyper- vs. hypo-5modC across tissues.

(D) Enrichment of hyper- (left) and hypo- (right) 5modC tissue-specific CpGs in full-stack ChromHMM states (false discovery rate [FDR] < 0.05). Circle sizes represent −log₁₀(FDR-adjusted p values) from one-tailed Fisher’s test.

(E) Heatmap showing enrichment (log₂ odds ratio) of tissue-specific hypo-5modCs (columns) in transcription factor binding sites (rows). Row labels are colored when the transcription factor is tissue specific and enriched in the matching tissue-specific CpG sets.