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Fig. 3 | Genome Biology

Fig. 3

From: Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome

Fig. 3

A visualization of Avocado’s learned latent representations. a A UMAP projection of the genome embeddings found at promoter (blue) and enhancer (orange) regions. Half of all promoter regions are shown along with an equal number of enhancers, which made up roughly one-fourth of total enhancers. Three manual partitions are shown, one with mainly promoters (85.5%), one with mainly enhancers (85.9%), and one that is mixed (44.9% promoters and 55.1% enhancers). b Average epigenomic profiles of H3K4me3 (red) and H3K27ac (blue) in promoters and enhancers in each of the three partitions, with the profiles extended out ± 2 kb to show additional context. c A UMAP projection of the assay embeddings, annotated with their name. Marks are colored to indicate enrichment in transcribed regions (green), association with active expression (pink), or association with repressing expression (orange). Marks that are not well characterized are colored in gray. d A UMAP projection of the cell type embeddings, where each cell type has been colored according to its anatomy type

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