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. 2024 Nov 22;56(12):2704–2717. doi: 10.1038/s41588-024-01961-x

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© The Author(s) 2024

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 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/.

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Extended Data Fig. 3 — a, DMEs that are upregulated in all disease conditions compared to control. Modules are grouped into different plots based on which disease condition had the highest effect size. Higher fold change values correspond to modules that are upregulated in disease. b, DMEs that are upregulated in one condition and downregulated in at least one other condition. c, Selected pathway enrichment results for the top 25 hub genes for each module for the set of modules upregulated in different disease conditions. d, DMEs that are downregulated in all disease conditions compared to control, similar to a. e, DMEs that are downregulated in one condition and upregulated in at least one other condition. f, Selected pathway enrichment results for the top 25 hub genes for each module for the set of modules downregulated in different disease conditions. g, Upset plot showing the overlap between sets of differentially expressed modules in each disease group. One-sided Fisher’s exact test was used for enrichment analysis.