Fig. 3
Fold changes in gene expression post spinal cord injury group by functional family. While fold changes in gene expression were already calculated and presented, genes were grouped together by their predetermined functional family (see Table 1) for better visualization of which family exhibited the most dynamic change post-injury. Genes encoding factors known to be involved with the immune and inflammatory process are grouped together (a), Genes encoding known growth factors and surface receptors are grouped together (b), Genes representing genes that are known to be pro or anti apoptotic are grouped together (c), and those genes that encode known neuroprotective or regeneration associated genes are grouped together (d). As can be seen in a–d, TPS neurons exhibited significant upregulation of genes across all four functional groupings. LDPT neurons receiving a T2 lesion exhibited a significant upregulation in three of the four genes (Fcgr2b, Itgam, and Lgals3) in the immune and inflammatory family (a) and two of the  five genes (Dap and Pycard) in the pro/anti apoptotic family (c), whereas in the growth factor and surface receptor family, two of the seven genes (Lifr and Ncam1) exhibited a significant downregulation in expression (b). In regards to the regeneration associated and neuroprotective genes family (d), of the 10 genes examined, one gene (Tspo) was significantly upregulated, one gene showed a trend towards significance (Atf3), and four genes (Gap43, Hspb1, Stmn2, and Tubb3) demonstrated a significant downregulation. LDPT neurons receiving a T10 level injury, were relatively quiescent, with significant changes in expression being found for only four of the total genes. This clustering of genes by family shows the most dynamic response in LDPT neurons receiving a T2 injury were among the genes involved with inflammation and the immune response, followed by the genes associated with neuroprotection and regeneration. Genes exhibiting a statistically significant fold change in expression compared to the uninjured control (corrected p value ≤ 0.10) 3 days post-injury are indicated by an asterisk (*). Gene trending towards significance but sample expression variability among the control group prevents statistical significance (#)