Fig. 3

Differential gene expression analysis of GF versus SPF fetal brain. A PCA of 1000 most variable genes. The ellipsoid shows Hotelling’s T2 (95%). B ORA of genes which were significantly upregulated or downregulated in GF versus SPF (p.adj < 0.05; DE GF up and DE GF down). The top 20 enriched ontology terms are shown; for more details, see Additional file 2: Fig. S1, S3. C Hallmark gene sets enriched in GSEA. A maximum of 10 of the top gene sets with FDR q-value < 25% are shown with negative (blue) and positive (red) net enrichment scores (NES) for GF versus SPF. D Volcano plot of differential gene expression. Genes with negative log₂ fold change values were downregulated in GF fetuses. Dashed lines indicate log₂ fold change ± 0.5 and adjusted p value 0.05