Fig. 2

Microglia states have diverse gene expression and biological pathway correlates. (A) UMAP of unbiased clustering on the cells from the four sorted clusters (5, 6, 7, and 13, shown in Fig. 1E) meeting criteria for microglia from the 9-sample dataset contains 12 microglia clusters. (B) Proportions of all microglia subclusters among three groups. (C) Differential expression analysis comparing each cluster to others demonstrates distinct gene expression profiles. The top 25 genes from each cluster are displayed with gene names annotated on the right. (D) GSEA analysis of genes that differentiate each cluster from cluster 9 (‘homeostatic microglia’) suggests distinct biological pathways. Permutation-based FDR was used for multiple testing of significance