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. 2021 Aug 24;12:710608. doi: 10.3389/fimmu.2021.710608

Figure 2.

Figure 2

Inflammatory gene expression in injured cortex is primarily altered by TBI. NanoString analysis using a mouse Immunology panel was used to assess cortical transcriptional patterns at 24 hours post-injury in young sham, aged sham, young TBI, and aged TBI mice (n=6/group). (A) A principle components analysis of all transcripts by subject identifies key genes changed by TBI (PC1) and age (PC2). There was no overlap and minimal within group variability in this analysis. (B) Expression map of the top 20 transcripts that were significantly altered by TBI only. 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. All transcripts that were significantly altered by TBI only are shown in Supplemental Table 1. (C) Dot plot of biological function GO terms enriched in the group of transcripts that was significantly altered by TBI only (R2>0.85), with no significant covariate effect of AGE. 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 gene ontology (GO) term and total number of genes assigned the term. There was no secondary thresholding for injury coefficients. (D) All transcripts that were significantly altered by injury (and the respective p-values for injury effect) were analyzed with Ingenuity Pathways Analysis to determine which canonical pathways were represented, and assign a z-score to indicate pathway activation (positive z-score) or deactivation (negative z-score). The top canonical pathways (-log p value of ≥ ≤ 5.0. with z scores >2 or <-2) are represented. All were positive (activated=blue bars), except LXR/RXR which was negatively regulated (deactivated=green bar). Individual z-scores and the genes that contribute to each canonical pathway are shown in Supplemental Table 5.