Figure 2. Transcriptional heterogeneity in human microglia.

a. UMAP of 8,662 microglia cells after removing putative infiltrating cells. Colors show 4 clusters defined using Louvain clustering (Materials and Methods). b. Microglial population variation between patient pathologies. The four different colours in Figure 2a illustrate population compositions for each pathology. Points coloured gray are all other cells. c. Heatmap shows the enrichment (log odds ratio) of microglial populations between pathologies d. Heatmap of averaged, normalised expression level (defined as the posterior mean of pathology random effect term, see Materials and Methods) of differentially expressed genes at local true sign rate (ltsr) greater than 0.9 (see Materials and Methods for details). Heatmap is divided into groups based on all possible pairwise groupings of the four cell populations, with the most transcriptionally distinct population at the top. e. Pathway enrichment analysis of differentially expressed genes between different microglial populations. The x-axis shows the P-value obtained by gProfiler2 with multiple testing corrections (Materials and Methods). Bars are coloured according to the combinations of clusters in which genes are upregulated. The upregulated cluster IDs are also shown besides the bars.