Fig. 2

Transcriptome analysis of HGF-induced microenvironmental changes in the spinal cord. a Principal component analysis of the gene expression data in rats at 2 days and 7 days after SCI, with or without HGF administration. The spatial arrangement of the points in the plot reflects the overall data similarity between the samples. x-axis, principal component (PC) 1 (55.86%); y-axis, PC2 (20.15%). b Differentially expressed gene (DEG) profile investigation using RNA-seq. Significant genes were selected with a cutoff, p < 0.05, and fold change > 2.0. day-2 HGF vs. day-2 control comparison: 929 DEGs, 752 upregulated, 177 downregulated; day-7 HGF vs. day-7 control: 3156 DEGs, 2047 upregulated, 1109 downregulated. c, d Dot plot showing the top 20 most significant GO biological process terms associated with upregulated expression in the day-2 HGF group compared with the day-2 control group (upper row). The enriched GO terms of the biological process are increased in the HGF group (lower row). e Heatmap of the expression values of neurogenesis-related genes in the day-2 control and HGF groups. Scale: z score of gene expression. f, g Dot plot showing the top 20 most significant GO biological process terms associated with downregulated expression in the day-2 HGF group compared with the day-2 control group (upper row). The enriched GO terms of the biological process are decreased in the HGF group (lower row). h Heatmap of the expression values of inflammatory-related genes in the day-2 control and HGF groups. Scale: z score of gene expression. Adjusted p value: adjusted p value by FDR, Intersection size: The number of unique DEGs that are annotated to the term ID. Gene ratio: calculated as the ratio of intersection size and query size