Fig. 2: Homeostatic microglia clusters.

a Cluster dendrogram calculated considering the average expression values of all cells/nuclei for each cluster and the unique gene markers for all clusters (distance: “spearman”; clustering: “ward.D”). The box highlights the three grouped clusters that show homeostatic microglia profiles. b UMAP representation of the three clusters annotated as homeostatic microglia. Cluster 0, Homeos1; Cluster 4, Homeos2; Cluster 8, Homeos3. c Dot plot representation of the expression of the top 10 most significant upregulated markers (ordered by avg_log2FC) for the three homeostatic cluster, within the full HuMicA object. The red dashed boxes highlight the top 10 markers for each cluster. The gene expression values correspond to the normalized “RNA” assay of the Seurat object. d Net plot representation of the three most significant gene ontology (GO) terms enriched for the respective markers of the three homeostatic clusters. GO was calculated using enrichGO package followed by the simplify function. The significance of the enrichment is represented in function of the negative of the log of the adjusted p-value (Benjamini-Horchberg). The range of expression of each gene associated with the GO terms is represented by the avg_log2FC. e Representation of the enrichment of the statistically significant (FDR < 0.05) transcription factors (TFs) relative to the comparison of differential expression of each HuMicA homeostatic clusters vs all other. Significance is represented by the normalized enrichment score and the negative of log of the adjusted p value (Benjamini-Horchberg). All presented TFs showed statistically significant enrichment, and the red dashed boxes highlight the TFs with an FDR < 0.05 for each of the homeostatic clusters. Source data are provided as a Source Data file.