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. 2022 Nov 14;23:481. doi: 10.1186/s12859-022-05005-1

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© The Author(s) 2022

Open AccessThis 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. 3 — The relationship between pathway overlap and significance. The artificially enriched pathway (R-HSA-1483206) is represented by a red cross. Overlap coefficient values of each pathway with R-HSA-1483206 are shown on the x-axis. t-test p-values of pathway scores (testing for significant difference in mean pathway score between disease and control group) for each pathway are shown on the y-axis (-log10 scale). Note, for GSEA the p-values are calculated using the original GSEA permutation procedure, and for ORA, p-values are calculated using the Fisher’s exact test. A LOWESS regression line is shown in black. Point size corresponds to the coverage of each pathway (i.e. the number of metabolites in the pathway which were present in the dataset)