Fig. 4

Gene expression patterns during infection time course. UMAP generated plot of F. nucleatum infection at time points 0, 2, 6, 12, 24, and 48 hrs with the following settings: row normalization, removal of zeros, number of neighbors = 15, minimum distance = 0.10, distance metric = Cosine, minimum expression = 1. Data points (genes) colored by a type, b type with continuous color setting, and expression of enrichment in c 0 h and 48 h. d Selected genes of interest graphed using GECO. e Data points (genes) colored by expression of enrichment in 6 h with minimum expression = 150 and 1.5-fold cutoff filter (See Additional file 3: Fig. S2a for UMAPs of addition step-by-step changes in filtering). Small subset of remaining genes following filtering with 4 genes highlighted with a red dot (TWIST2, ICAM1, CXCL3, and NINJ1) that are enriched in 6 h and 2 h infection time points. f Correlation of F. nucleatum infection related genes displayed in a GECO generated clustermap. Dark teal boxes with an asterisk are significantly positively correlated in expression across all samples (ex: ICAM1 and CXCL3), whereas dark brown boxes with an asterisk are anti-correlating across all samples (ex: COL1A1 and SOD2). Previously published bulk RNA-seq of F. nucleatum infection time course [24] was used to generate UMAP clustering and this dataset (.csv file) is available in Additional file 5