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. 2022 Dec 21;10:188. doi: 10.1186/s40478-022-01494-6

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© The Author(s) 2022

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 6 — AD pathology-associated gene signatures and pathways. (A) Heatmap of Z-scores for upregulated and downregulated DEGs specific to Visium spots localized with different AD pathologies (Aβ⁺, AT8⁺, and Aβ/AT8⁺). DEGs were identified from pathological regions (either Aβ⁺, AT8⁺, and Aβ/AT8⁺) vs. surrounding level 3 spots of three AD samples at the pseudo-bulk level. The red color indicates a relevantly higher expression than other pathologies, while the blue color indicates a lower expression. (B) Gene ontology (GO) pathway analysis of identified DEGs (Additional file 10: Table S9) specific to Visium spots localized with Aβ plaques (top row) or pathological tau, AT8 (bottom row). The Dot plot shows top 10 enriched GO terms. Each dot is colored by the Benjamini–Hochberg adjusted p-value. The dot size is scaled by the number of overlapping genes with the related GO terms. The x-axis is the ratio and indicating the proportion of overlapping genes between the query gene list and all genes in the GO term