Fig. 6: Integrative analysis of Spi1-mediated transcriptomic alterations.
DEGs in Spi1+/−;APP/PS1 (KD) versus Spi1+/+;APP/PS1 (WT) and Spi1Tg/0;5XFAD (TG) versus Spi1+/+;5XFAD (WT) mice were analyzed with a linear regression model for genotypes. a Workflow for LIMMA analysis. Transcription factor enrichment analysis (b) and Pathway enrichment analysis (c) with combined DEGs were performed using the MetaCore software. P-values of b and c were calculated using Metacore algorithms with a threshold of significant enrichment as p < 0.05 (shown as a vertical dash line for b and c). d All DEGs were summarized in a Venn diagram, which identified six shared DEGs across Spi1+/−;APP/PS1 versus Spi1+/+;APP/PS1 mice and Spi1Tg/0;5XFAD versus Spi1+/+;5XFAD mice. e Relative expression levels of six shared DEGs. Quantification data were expressed as log2FC of expression relative to each control group. All values are mean ± SEM (n = 3 per group). f A protein-protein interaction network was generated using the STRING database for the combined DEGs (63 genes) and Spi1. The data showed interactions with Spi1 and among all DEGs. Wider lines represent stronger evidence of interactions. g Integrative pathmap analysis was performed using both sets of DEGs using MetaCore. Up-regulated genes in our dataset are shown with red circles, down-regulated genes are shown with blue circles, and the mixed-signal gene is shown with a red-blue mixed circle in the pathmap. Green arrows between nodes represent activation, while gray arrows represent interaction with no specific direction of effect. DEGs shown are involved in the immune response and complement system. Source data are provided as a Source data file.
