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. 2023 Mar 9;3(3):327–345. doi: 10.1038/s43587-023-00373-6

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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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Fig. 4 — a, Rose diagrams (circular histograms of number of DGEs) of aging, RJV and AGA across all cell types at FDR ≤ 0.05, colored by direction of log(FC) (up magenta, down blue). b, Venn diagram of RJV and AGA DGEs across all cell types, demonstrating bidirectional log(FC) changes between the comparisons (depicted with arrows). c,d, Upset plot of FDR = 0.05 DGE with positive log(FC) (upregulation) and negative log(FC) (downregulation) in both RJV (c) and AGA (d). The top bar height reflects the number of DGEs in the intersection (in common between the barbells below), and the side bar width reflects the magnitude of the set size. e, EC RJV and AGA DGE Venn diagram split by log(FC) sign, revealing genes that reverse direction between comparisons. The arrows point to listed bidirectional genes. f, GSEA dot plots (Benjamini–Hochberg-adjusted P value for multiple comparisons (P_adj) ≤ 0.25) of representative terms across cell types in RJV and aging, with the size of dot proportional to inverse P_adj and color by NES from negative (blue) to positive (magenta).