Fig. 1

Characterization of SE-associated gene signatures of patient-derived primary G3-MB lines. a Enhancer profile of five G3-MB lines based on H3K27Ac ChIP-seq signal in reads per million per base pair (rpm/bp). Enhancers are ranked by increasing H3K27Ac ChIP-seq signal. Super enhancers (SEs) are highlighted in red with ranks of selected SE-associated genes. b Gene tracks of H3K27Ac ChIP-seq signal across five G3-MB lines at SE regions near MYC, OTX and CRX. SE regions are depicted in colored lines over the gene tracks. c Venn diagram analysis of SE-associated genes from the five G3-MB cell lines. d Venn diagram showing overlapping SE-associated genes (oSE) of tSE and cSE. e Gene ontology (GO) analyses of genes of cSE, tSE and oSE. The biological process (BP) cluster comparation analysis was performed with Cytoscape plug-in ClueGo. f-g Violin plots showing log2_FC (fold change) of gene expression (left Y axis) or dot plots showing percentage of significantly upregulated genes (right Y axis) for genes in all, cSE, tSE and oSE categories, when comparing G3-MB tissues with normal cerebellum (NC) in f (log2_FC > 1, FDR < 0.05) or the other three MB subtypes in g ( log2_FC > 0.5, FDR < 0.05) in the indicated MB datasets. h Violin plots showing CERES gene effect score (left Y axis) or dot plots of percentage of genes with CERES gene effect score < -0.1 (right Y axis) in all, cSE, tSE and oSE categories in the indicated G3-MB lines. i Violin plots showing GSVA score of oSE genes in four MB subgroups or NC of the indicated MB datasets. j Kaplan-Meier survival analysis of the GSVA scores of oSE genes in Cavalli dataset of MB. The patient cohort was stratified as high versus low groups based on median GSVA score. Statistical significance was determined by one-way ANOVA (f-i) or two-sided log-rank test (j), respectively