Fig. 1

Differential gene expression and gene set enrichment analysis of OA macrophages. Volcano plots showing the top differentially expressed genes of macrophages at 4-weeks (A) and 12-weeks (B) post surgery, as compared to sham controls. The Y-axis represents the -log10 of the adjusted p-value with a cut-off set at 1.3 (padj < 0.05) and the x-axis represents the log2 fold change with cut-off at -0.5 and 0.5. Bubble plots showing gene set enrichment of Gene Ontology terms at 4-weeks (C) and 12-weeks (D) and enrichment of Hallmark term at 4-weeks (E) after OA induction versus sham controls. LOGGY represents the -log10 of the false discovery rate (FDR <0.05) and Rich.Ratio the number of genes called to a set divided by the total number of genes in the set. Venn diagrams comparing the number significantly enriched hallmark pathways in early-stage OA development (shown in panel E) that are associated with STAT signaling and their overlap with pathways involving MAPK, PI3K, and SMAD signaling mechanisms (F)