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. 2024 Dec 4;14:30202. doi: 10.1038/s41598-024-80534-8

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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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Fig. 1 — Differential gene expression analysis and pairwise analysis of the discovery cohort. (A) Schematic of the differential expression analysis and pairwise analysis. (B) Workflow of differential expression analysis and ranked position of the top 100 differentially expressed genes and bottom 100 genes in NR when ranked by t-stat and the position of these genes when ranked by LogFC and combined. (C) Venn diagram of the significant Hallmark signatures (padj < 0.05) from GSEA when genes were ranked by t-stat, LogFC, and combined. (D) Significant Hallmark signatures (padj < 0.05) identified from clusterProfiler GSEA when genes were ranked by t-stat, LogFC, and LogFC combined with the p-value ordered by NES. (E) clusterProfiler GSEA, fGSEA, and GenePattern pre-ranked GSEA of the significant Hallmark gene sets. Enrichment plots from (F) clusterProfiler GSEA, (G) fGSEA, (H) GenePattern comparing NR CC (n = 142) to R CC (n = 73) for Interferon Alpha Response, Interferon Gamma Response and EMT.