Extended Data Figure 10 : Putative cell lineage programs of origin uncovered by transcription factor mapping.

From: Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

Extended Data Figure 10

ac, Immunohistochemical staining of Foxj1 at day 13.5 of mouse embryonic development (E13.5). Staining in discrete regions encompassing the choroid plexus and ependymal layer are shown in the forebrain (b) and hindbrain (c). d, log2 normalized gene expression of FOXJ1 in ependymoma (n = 83 independent samples) compared to independent sample cohorts of the following tissue types: normal brain (n = 172), paediatric glioma (n = 53), glioblastoma (n = 84), atypical rhabdoid teratoid tumours (n = 18), medulloblastoma (n = 62) and pilocytic astrocytoma (n = 41). Horizontal bar indicates the mean value. e, Subgroup-specific gene expression of FOXJ1 derived from ref. 1 (n = 209 independent samples). Error bars indicate s.d. and interquartile range; horizontal bar indicates median. f, Gene set enrichment analysis30 demonstrating significant enrichment of the FOXJ1 transcriptional program derived from E14.5 mouse embryos specifically in PF-EPN-B tumours (n = 209 independent samples). FDR corrected significance evaluated by gene set enrichment analysis. g, Significant FOXJ1 gene-expression correlations with proteins known to regulate cilia assembly and function. P values for significant positive or negative correlations have been corrected for multiple testing using the Bonferroni method. hm, FOXJ1 gene set enrichment plots of PF-EPN-A (h), PF-EPN-B (i), PF-EPN-SE (j), ST-EPN-RELA (k), ST-EPN-YAP1 (l) and ST-EPN-SE (m) ependymomas. FDR-corrected significance evaluated by gene set enrichment analysis, n = 209 independent samples.