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. 2023 Nov 13;26(12):2104–2121. doi: 10.1038/s41593-023-01480-8

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 8 — a, Feature plot showing relative levels of normalized human APOE gene expression across all 12 astrocyte subclusters by APOE genotype from mice at 10 months of age. b–d, KEGG pathway enrichment dot-plot of top 20 pathways significantly enriched for DE genes of astrocyte subclusters 3 (b), 5 (c), and 7 (d) versus other astrocyte subclusters. e, Feature plot showing relative levels of normalized human APOE gene expression across all 15 microglia subclusters by APOE genotype from mice at 10 months of age. f–h, KEGG pathway enrichment dot-plot of top 20 pathways significantly enriched for DE genes of microglia subclusters 2 (f), 8 (g), and 11 (h) versus other microglia subclusters. In b–d and f–h, P-values are based on a two-sided hypergeometric test and are adjusted for multiple testing using the Benjamini-Hochberg method. Gene Ratio represents the proportion of genes in the respective gene set that are deemed to be differentially expressed using the two-sided Wilcoxon Rank-Sum test as implemented in the FindMarkers function in Seurat.