Fig. 2: Transcriptomic dysregulation in the PolyI:C mice model.
From: Increased RNA editing in maternal immune activation model of neurodevelopmental disease
a Heat map of the 50 most differentially expressed genes (i.e. smallest FDRs) using normalized (separate Z-score computed per gene) TPM expression values. b Volcano plot representing the expression changes of all genes. Significantly down- and upregulated genes (log2 FC|>1 and FDR < 0.05) are colored navy and red, respectively. Genes that do not show significant expression changes are colored gray. Top 10 most differential genes (i.e. smallest FDRs) are labeled with gene names. c PCA analysis. Principal components were computed for each sample using gene expression. The first two principal components (PC1 and PC2) are shown. The percent of variance explained by each component is reported in parentheses. d Gene set enrichment analysis performed on gene ontology (GO) terms, identified down- and upregulated gene sets. Each node represents one gene set (i.e. a GO term) where the node size indicates the number of genes in the gene set and the color indicates down- (blue) or up- (red) regulation. In summary, the data nodes are clustered based on the number of shared genes between any two gene sets (using the Enrichment map plugin on Cytoscape—see Methods). Three biological modules emerge: (I) neuronal development, (II) metabolic/energy, and (III) immunological. The distances between the nodes and edge thickness indicate the number of shared genes (closer and thicker indicate more shared genes). The following are the largest gene sets in each module: GO FOREBRAIN DEVELOPMENT, GO NUCLEOBASE CONTAINING SMALL MOLECULE METABOLIC PROCESS, and GO REGULATION OF CYTOKINE PRODUCTION for modules I, II, and III respectively. A full list of the gene sets included in this plot are presented in Supplementary Data 3. Source data are provided as a Source Data file.
