Fig. 2

Differential gene expression (DGE) analysis of CC samples from lithium-treated and untreated rats. a MA-plot showing the relationship between mean expression values and fold changes for all analyzed genes. Each dot represents a gene. Significantly associated genes (FDR < 0.05) are colored in red, and the 10 most significant genes (lowest FDR value) are labeled. As the plot shows, the effect size variance is dependent on the mean expression value. Genes with lower average expression tend to have bigger fold changes between conditions, indicating the increased uncertainty in effect size estimates of low-abundance genes and the need for pre-filtering. b Volcano plot showing the fold change and p-value for each gene. Genes with significant up-regulation (FDR < 0.05) in lithium-treated rats are colored in red, and genes with significant down-regulation are colored in blue. The 10 genes with the lowest p-values are labeled. c Biotypes of lithium-associated DGE genes. The majority of genes were protein coding. Small RNAs include miRNAs and snoRNAs. “Other” include pseudogenes and processed pseudogenes. lncRNA: Long non-coding RNA. d Grouping of significantly enriched DGE pathways according to the KEGG subcategory arrangement. Most of the enriched pathways were involved in signal transduction processes (n = 7) and immune system functions (n = 4). KEGG: The Kyoto Encyclopedia of Genes and Genomes