Fig. 1: Activity-dependent genes are expressed after stroke.

a Experimental timeline. b FACS plots from groups that correspond to treatments and timelines in (a), showing gating and selection of NCAM+ve events that are also positive for fluorescence expression carried by the viral construct (events that fall in the Q2 quadrant). c Gene set enrichment, FDR < 0.1, for various activity-dependent gene sets (y-axis) across conditions compared to Naïve (groups with *) or treatment groups compared with controls that received the same viral backbone. Set size denotes the number of genes in each gene set denoted by the size of the circle: positive enrichment in warmer colors and negative enrichment in cooler colors. d Scatter plot showing behavioral scores for each of the conditions compared to Naïve and their corresponding enrichment scores compared to Naïve for the various activity gene sets in (c). Increasing behavioral scores corresponds to increases in motor deficits. The line drawn represents the line of best fit and gray shaded region is the confidence interval around the slope of the regression line. e Classification of samples from untreated and treated groups before and after stroke using random forest classifiers trained on the various activity-dependent gene sets. Data are median ± SD of prediction error from five iterations. f Heatmap of row normalized gene expression (z-scores) of hierarchically clustered genes from gene sets from top-performing classifiers. Columns are individual samples from 3 groups (Naïve, Ctrl stroke acute, and CCR5kd stroke acute) and gene expression values in rows. g Model performance metrics for each classifier on training (gray) and test data (red). Data are mean values from each iteration with standard error.