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. 2021 Oct 15;12:6023. doi: 10.1038/s41467-021-26299-4

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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. 6 — a Computation pipeline of model construction of time-response interaction pathway-based Super Signatures. b The volcano plot of differential gene expression analysis of response pre-treatment and on-treatment samples in the Riaz et al. cohort. Log2Fold change (FC) was calculated. The two-sided Wald test was implemented to test if no differential expression between response pre-treatment and on-treatment samples. The blue dots represent significantly downregulated (Signif. downregulated) genes (log2Fold Change < −1, P-value < 0.05). The red dots represent significantly upregulated (Signif. upregulated) genes (log2Fold Change > 1, P-value < 0.05). The gray dots represent nonsignificant (NS) genes. c–e ROCs and AUCs of the time-response interaction pathway-based super signatures for pre-treatment samples (TimeANLS-PRE) from Riaz et al. cohort (c), Gide et al., Lee et al., and MGH cohorts (d), combined pre-treatment with Gide et al., Lee et al., and MGH cohorts (e). f–h ROCs and AUCs of the time-response interaction pathway-based super signatures for on-treatment samples (TimeANLS-ON) from Riaz et al. cohort (f), Gide et al., Lee et al., and MGH cohorts (g), combined on-treatment with Gide et al., Lee et al., and MGH cohorts (h). Source data are provided as a Source Data file.