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Fig. 4 | Genome Biology

Fig. 4

From: Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues

Fig. 4

Differential distribution of DNA marks between GSC and NSC. a Phyloepigenetic evolutionary tree demonstrating the progression and relationship of the DNA methylation landscape from normal tissues/cell lines, to primary tumors, and GSCs isolated from the primary tumor. Black: normal tissue/cell line; orange: TCGA-mesenchymal subtype; green: TCGA-proneural; blue: TCGA-classical; purple: TCGA-neural; red: PDX-derived GSCs; blue: PDX primary tumor. b Stacked bar graph showing the proportion of low, medium, and highly modified CpG sites for 5mC, 5hmC, and 5fC/5caC. Cutoffs for defining highly/lowly modified sites are: 5mC, 0.6/0.2; 5hmC: 0.15/0.05; 5fC/5caC: 0.2/0.1. c Ring-bar graph depicting enrichment of highly modified 5mC (top), 5hmC (middle), and 5fC/5caC (bottom) sites at CpG islands (CGI), shores, shelves, and sea for NSC (outside) and GSC (inside). d Bar graph illustrating enrichment (normalized to the total number of CpGs associated with each feature, noted in the center panel) of differential modification events between GSC and NSC on average. Hyper-modification events are denoted by positive values, hypo-events by negative values. Y-axis enrichment level. X-axis genomic features, as shown for 5hmC. e Density scatter plots showing switching events at the same CpGs between NSC and GSC for 5mC and 5hmC (left), 5hmC and 5fC/5caC (middle), and 5mC and 5fC/5caC (right). Red dashed line indicates the cutoff for differential modification of 5mC (0.25), 5hmC (0.05), and 5fC/5caC (0.05). Histograms and boxplots demonstrate the distribution pattern of each mark. X-axis and Y-axis indicate levels of modification change for each mark. N number of events in each quadrant

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