Fig. 3

Network analysis and visualization of pseudotime trajectory. a Simple feed-forward loops (SFFLs) of microRNAs, transcription factors and target genes, as well as merged networks (MFFLs) for the same center node and their distribution among cell clusters. Number of microRNA families with significant loss of binding sites for respective cell cluster is indicated. b Upset plot showing the overlap of significant SFFLs among cell clusters. c Manually curated list of enriched pathways for genes and transcription factors involved in MFFLs in OPC and neoplastic clusters, computed with Reactome and Wiki pathways. d Kaplan–Meier plot based on GBM-TCGA data. e UMAP of filtered neoplastic cells and OPCs f Pseudotime trajectory analysis for neoplastic cell to OPC differentiation. g MFFL networks of microRNA, TF, and target gene containing genes involved in differential APA events and differential gene expression derived from pseudotime analysis and significant for neoplastic cells