a– c, 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, log 2 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 analysis demonstrating significant enrichment of the 30 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. h– m, 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.