Skip to main content
. 2023 Oct 14;26(11):108213. doi: 10.1016/j.isci.2023.108213

Figure 5.

Figure 5

Strain-specific differences are found in intrahepatic myeloid cells

(A) Expression pattern of the top DA-enriched genes (Ly6al, Cd163, Hmox1, Siglec5) over PC15 and 1. LEW and DA myeloid cells have been marked with dotted circles. Dark green indicates higher expression values. Comparison with Figure 2F confirms that the selected genes have higher expression in the DA strain compared to LEW.

(B) Expression pattern of the top LEW-enriched genes (Itgal, Il18, Ccl3, Timp2) over varimax-15 and 1. Comparison with Figure 2F confirms that the selected genes have higher expression in the LEW strain compared to DA.

(C) Dot plot indicating the relative expression of strain-related genes within the myeloid fraction (clusters 5, 10, 9) of each strain. The top 10 genes with positive (LEW-associated) and negative (DA-associated) varimax-15 loading scores have been selected. The size of the circle indicates the percentage of cells in each population expressing the marker, and its color shows the average expression value.

(D) Pathway enrichment analysis using GSEA (gene set enrichment analysis) to examine active cellular pathways in LEW vs. DA myeloid cells based on varimax-15 loadings visualized as an enrichment map. Each circle represents a gene ontology (GO) biological process term. The size of the circles represents the number of genes in that pathway, and blue lines indicate significant gene overlap. Since PC15 is positively correlated with the LEW strain and negatively correlated with DA, red circles represent activated pathways in LEW and blue indicates upregulated pathways in DA. No pathway was significantly upregulated in DA.

Transcriptional factor (TF) binding site-based gene set enrichment analysis using gProfiler on the ChEA ChIP-Seq database identifies TFs which may be activated in (E) DA and (F) LEW myeloid cells. TFs are sorted based on their enrichment significance calculated as –log10(adjusted p value). Dark purple indicates higher significance. Purple boxes highlight TFs which are uniquely enriched in that strain.