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. 2021 Jul 27;12:4567. doi: 10.1038/s41467-021-24807-0

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© The Author(s) 2021

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. 5 — a, b Gene set enrichment analysis (GSEA) of clusters 1–4 of the M1 route a. and M2 route b. using public transcriptome data, including post-mortem lung tissue from a COVID-19 patient (GSE147507) and lung tissue from a SARS-CoV-2-infected mouse (GSE150847). For calculating combined scores, upregulated genes derived from COVID-19 patients’ lung tissue and SARS-CoV-2-infected mouse lung were compared to the marker genes of pseudo time clusters of M1 or M2 route, which was calculated from the p value obtained using Fisher’s exact test and the z-score (see “Methods”). Commonly upregulated genes are listed in the box right side of each bar graph. c Experimental design to make dexamethasone and etanercept responsive gene sets for GSEA of clusters 1–4 of the M1 and M2 route. d, e GSEA of clusters 1–4 of the M1 route (c) and M2 route (d) using ranked gene list originated from dexamethasone-downregulated DEGs derived from in vitro experiment described in (c). The name of genes included as core enrichment was listed, NES normalized enrichment score. The p values of the combined score are calculated with a two-sided Fisher’s exact test. The p value of GSEA is the probability under the null distribution calculated by the permutation test. Source data are provided as a Source Data file.