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. 2021 Jan 12;22:22. doi: 10.1186/s12859-020-03929-0

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© The Author(s) 2021

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 — Comparisons between dpGSEA show statistically significant differences between enrichment results. Plots a–d show trends and comparisons between dpGSEA (a, c) and GSEA (b, d) for the top 20 and top 50 p value ranked proto-matrices (derived from LINCS data) identifying positively correlated genes. Plots a and b compare the top 20 ranked proto-matrices between dpGSEA and GSEA with each point representing an enriched drug in the final generated list. The labeled blue points all denote paclitaxel perturbated cell lines for the GEPNTs paclitaxel perturbation versus a GEPNTs DMSO control DE. The x-axis represents − log10 of the enrichment score (ES) p value and the y-axis − log10 of the target compatibility score (TCS) p value of corresponding perturbated drug cell line combination. The sub-axis lists the order of ascending significance for ES and TCS, respective of axis, that are also shown in tables E. The tables compare between the ranked orders for both ES and TCS with Wilcoxon signed rank test p values, suggesting the difference between dpGSEA and traditional GSEA results