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. 2023 Jul 12;13:11. doi: 10.1186/s13395-023-00321-3

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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 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. 1 — Summary of the analysis. A Flowchart for identifying age-related genes, pathway enrichment analysis, and transcription factor (TF) association analysis. RNA-seq data were processed from each species, sex, and tissue separately. The raw gene expression counts were normalized using the limma package, and the normalized data were used to first identify differentially expressed (DE) genes. Genes were considered differentially expressed if their expression was upregulated or downregulated by ≥ 1.5 fold at any age compared to 6 months, with the adjusted p value of > 0.05. To define age-related genes, we fitted the trend of a DE gene by null, linear, and a 4-parameter logistic model. Bayesian information content (BIC) was used to identify the best model among the three, and DE genes with a linear or a logistic trend were considered age-related. Next, age-related genes, with linear and logistic behaviors were used to perform pathway enrichment analyses and transcription factor (TF) motif enrichment. B Examples of age-related genes that follow a linear pattern, or early, mid-, or late-logistic patterns (shown for the mouse gastrocnemius)