Figure 3.

Analysis of C134-induced changes in immune cell infiltrate and gene expression in medulloblastomas

(A) Cell type proportions in C134 vs. vehicle-treated medulloblastomas. Differences in each respective cell type’s proportions in C134 vs. vehicle-treated samples were statistically evaluated using t-tests after logit-transformation and using an empirical Bayes framework. ∗Denotes a false discovery rate (FDR) of less than 0.05 (B) Inclusion criteria for genes were an average log2-fold change (Log2FC) of greater than 3 or less than −3 and an adjusted p value of less than 0.05 in any of the six immune cell types shown. The expression of these genes is shown for all immune cell types on the heatmap regardless of Log2FC, however, values with an adjusted p value of greater than 0.05 are colored in gray. Volcano plots show results of differential gene expression analysis performed on a cell type basis from pooling C134-treated and vehicle-treated samples for lymphocytes (C), mixed monocytes/macrophages (D), microglia (E), and DCs (F). Differentially expressed genes in (B–F) were evaluated using a Wilcoxon rank-sum test.