Fig. 2: Chromatin states classify bladder cancers by subgroups. | Oncogene

Fig. 2: Chromatin states classify bladder cancers by subgroups.

From: Epigenomic mapping identifies an enhancer repertoire that regulates cell identity in bladder cancer through distinct transcription factor networks

Fig. 2: Chromatin states classify bladder cancers by subgroups.

A ChromHMM principle example and emission order dividing genome in 6 states based on combination of H3K27ac, H3K27me3 and H3K9me3 marks. B Gene-expression level by chromatin state at transcription start site. C Two chromatin state clusters revealed by unsupervised analysis of top 1% varying regions using MDS for dimension reduction plus MNN for batch effect correction. D GSEA functional enrichment analysis of the genes mapped to the MCA Dim2 contributing features. A negative NES indicates significant enrichment in lower Dim2 coordinates (Basal direction), and the reverse is in higher Dim2 coordinates (Luminal direction). E Luminal versus basal tumour cell signature genes identified with single cell RNA-seq analysis showing concordant enrichment in chromatin state clusters. F Genome Browser view of chromatin states at FOXA1 and KRT6 loci with corresponding RNA-seq (VST normalized scaled expression). Regulatory regions of interest are highlighted with dashed-line rectangles.

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