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. 2022 Apr 5;16(7):1776–1787. doi: 10.1038/s41396-022-01230-x

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© The Author(s) 2022

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 Number of DE genes at a 5% FDR-level in the average response and the individual strains. The number of DE genes is indicated separately for each contrast, distinguishing between genes that are up or downregulated. B Direction of DE in the top 100 genes of the average response and individual strains as selected by p value or logFC. For each contrast in the average and individual strains (vertical black bar), the direction of DE is indicated for the top-100 genes selected by stageR’s FDR-adjusted p value of the global null hypothesis (Padjscreen). Thus, although a gene can have a high p value on a dataset-wide level, it is not necessarily DE in each individual contrast. In addition, we show the top-100 genes selected by logFC (topconfects [100]) and the contrast-specific 5 % FDR-controlled p value (Padj) for the 8–24 contrast of the average effects, as this contrast showed the greatest number of DE genes in (A). C Number of enriched GO terms for the ORA and GSEA analyses. The number of up- and downregulated GSEA GO terms represents the output classification by CAMERA. The number of enriched GO terms includes Biological Process, Molecular Function, and Cellular Component GO terms, prior to removal of redundant GO terms by REVIGO.