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. 2024 Mar 8;20(4):374–402. doi: 10.1038/s44320-024-00024-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/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) Line charts depict four clusters (gray-scaled) of gene expression trends (z-score) for unified deregulated genes (DEGs, n = 1477) in mice on different diets and ER-agonist treatments (color-coded, n = 4, except PPT: n = 3). Cluster centroid (dashed black line) represents all deregulated genes (gray lines). Number of genes per cluster is shown (parentheses). (B) Three-way Venn diagram (left) presents intersections of unified DEGs (clustered in (A)). Genes are categorized (right) into non-reverted (rose), reverted (denim), ERβ-specific (DPN-DIP, ocher) and ERα-specific (E2-PPT, violet) gene sets. Horizontal bar chart displays the proportional occurrences of gene sets in the four clusters (gray scale as in (A)). Number (n) indicates gene set size. (C) PCA factorial map separates the semantic space of enriched gene ontology (GO) terms in reverted and ERβ-specific gene sets (circles). Enriched GO terms are collapsed at the parent term level and separated based on similarity (x–y axis). Circle size corresponds to number of enriched GO terms. A hypergeometric test with Benjamini–Hochberg correction was used for the overrepresentation analysis.