Figure 3.

Inflammatory gene expression in injured cortex is also altered by age alone or combined aged plus TBI. (A) Expression map of transcripts that were significantly altered by age only. Of these 12, only 4 had R2 values of >0.80 (Supplemental Table 2), indicating that the expression of this group contributed only minimally to the regression model. Biological function GO terms could not be assigned to this group, due to their small number. The heat map color scale reflects normalized log-transformed raw counts scaled to z-scores, where -1=darker blue=decreased expression and 1=darker yellow=increased expression. (B) Expression map of transcripts that were significantly altered by TBI and age (14 genes, 9 with R2 >0.80). The heat map color-scale reflects normalized log-transformed raw counts scaled to z-scores, where -1=darker blue=decreased expression and 1=darker yellow=increased expression. (C) Dot plot of biological function GO terms enriched in the group of transcripts that was significantly altered by TBI and age (R2>0.85). The list of individual genes and their significance values appears in Supplemental Table 3. The color of the dots is based on adjusted p-value (FDR) with the darker color (red) corresponding to higher/greater p-value, and lighter color (violet) corresponding to lower/smaller p values. The radius of the dots is based on the number of genes assigned to the term. The x axis corresponds to the gene ratio, which is the ratio of genes within the dataset represented within a given GO term and total number of genes assigned the term. There was no secondary thresholding for injury coefficients. The term “interspecies int. between organisms” is abbreviated from the full formal name = biological process involved in interspecies interaction between organisms, “reg. of resp. to external stimulus” abbreviated from = regulation of response to external stimulus, “pos. reg. of resp. to external stimulus” for = positive regulation of response to external stimulus, and “pos. reg. of NF-kappa B TF activity” for = positive regulation of NF-kappaB TF activity. (D) CIRCOs plot shows the involvement of genes from (B) with multiple roles in the biological functions defined in (C). The red and blue bars next to each individual gene indicate increased (red) or decreased (blue) expression of the gene, where intensity of shading indicates the relative change (dark/greater to light/less). Cebpb, Cx3cl1, Ccr5 and Csf1r have a wide range of functions, and were associated with 5 of the 6 GO terms.