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. 2023 Jan 9;3:5. doi: 10.1038/s43856-022-00231-3

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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 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. 3 — a A quantile–quantile plot of the p values of pathways in MSEA based on the KEGG pathways. The x-axis indicates log-transformed expected p values. The y-axis indicates log-transformed observed p values. The diagonal dashed line represents y = x, which corresponds to the null hypothesis. The horizontal red dashed line indicates the Bonferroni-corrected threshold (α = 0.05), and the brown dashed line indicates the FDR threshold (FDR = 0.10) calculated with the Benjamini-Hochberg method. Pathways with p values less than the FDR thresholds are plotted as brown dots. b Bar-plot of the Z-scores in case–control association tests. The x-axis indicates the rank of the metabolites according to their Z-score. the y-axis indicates the Z-scores of the metabolites. Rhombus indicates the metabolites which are annotated as fatty acid biosynthesis-related metabolites. The number of samples used for the analysis is N_{DR + DKD} = 141 and N_control = 159. DKD, diabetic kidney disease; DR diabetic retinopathy; ES, enrichment score; FDR, false discovery rate; KEGG, Kyoto Encyclopedia of Genes and Genomes; MSEA, metabolite set enrichment analysis.