Extended Data Fig. 3: Havcr2^cKO microglia share gene expression signature with Tgfbr2^cKO microglia, phagocytosing microglia, and MGnD.

a, Circos plot comparison of DEGs up- and down-regulated in Havcr2^cKO, phagocytosing, Tgfbr2^cKO, and Clec7a⁺ microglia compared to control microglia. Only islands with DEGs shared by at least 3 of the 4 comparisons were included. Permutation test p-values were displayed as ns P > 0.025, *P ≤ 0.025, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001, and *****P ≤ 0.00001. b, Heatmap visualization of DEGs shared by at least 3 of the 4 comparisons. c, Heatmap representation of the correlation between vectors of the gene expression levels of all DEGs of (1) Havcr2^cKO microglia compared to control microglia, and those shared by comparison (2) to (4) (phagocytosing, Tgfbr2^cKO, Clec7a⁺ microglia compared to their corresponding control groups).