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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. 5 — AD-associated gene modules and their co-expression patterns within areas of AD pathology. (A) Gene-ontology (GO) pathway analysis of four modules (Yellow, Turquoise, Pink and Brown) identified by weighted gene co-expression network analysis (WGCNA) of 10,000 highly variable genes from six samples (Additional file 1: Fig. S5). Dot plot shows top 10 enriched GO terms: biological process terms from the DEGs within each module (Additional file 9: Table S8). 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 scaled by the ratio between the overlapping count and the total number of genes of the term. Gene set enrichment analysis was performed using the Enrichr web server. (B) Circos plots of the connectivity strength within and across modules for Visium spots in CT human MTG and Visium spots in AD human MTG with specific AD pathology (Aβ⁺, AT8⁺, and Aβ/AT8⁺). Circos plots are composed of four different modules (Yellow, Turquoise, Pink and Brown; top 30 hub genes from each module based on their closeness centrality score); nodes represent highly deregulated genes from each module; and edges (green lines) indicate connectivity (high: dark green, low: light green)