Fig. 5

RNA-seq analysis in the cerebellar granule cell layer of Kdm3b^+/− mice. a Volcano plot of the differentially expressed (DEX) genes in Kdm3b^+/− mice compared to WT mice. Y axis is the false discovery rate (FDR) with − log10 used and X axis is the expression values of Kdm3b^+/− mice divided by WT mice with log2 used. Two mice per group were used for the analyses. b Gene ontology (GO) analysis of the down-DEX genes compared to wild type mice. Three GO domain, GO biological process (GO:BP), cellular component (GO:CC), and molecular function (GO:MF) were used. Results with term size equal to or bigger than 30 and less than 1000 were used. Y axis is the name of the terms of the GO results and X axis is the FDR with − log10 used. c GO analysis of the up-DEX genes compared to wild type mice. Results were filtered same as in (b). In b and c, the number in parentheses indicates the number of genes belonging to a given GO term. d Gene network analysis using 28 genes, which intersected with the GO term ‘regulation of trans-synaptic signaling’ (GO:0099177; p-value = 1.4E−02). The intersected genes are colored green. e RT-qPCR validation of selected DEX genes. RT-qPCR analysis targeted the six selected genes (Fam107a, Homer3, Fgf1, Car2, Cplx2, and Ntf3) was performed using GCE samples obtained from Kdm3b^+/+ and Kdm3b^+/− mice (n = 3 per group). An independent t-test was performed to test statistical significance between two groups. **p < 0.01