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. 2021 Oct 18;12:6053. doi: 10.1038/s41467-021-26289-6

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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. 3 — a Workflow of crude fractionation with subsequent proteome and phosphoproteome analysis of U937 cells. Gray = untreated, red = TNF, orange = TNF + TAK1 inhibitor. b Most quantified proteins are significantly enriched in one of membrane, nucleus, and cytosol fractions (two-sided Student’s t-test FDR < 0.05). c Total number of quantified phosphosites and the numbers of phosphosites significantly enriched in the three fractions (two-sided Student’s t-test FDR < 0.05). Class-I sites (in black) are phosphosites with a localization probability of > 75%. d Heatmap of means of z-scored protein intensities enriched in the membrane upon TNF treatment (two-sided Student’s t-test, -Log10 p > 1.29, Log2 fold change > 0.5). e Heatmap of means of the 20 most strongly up- and downregulated z-scored protein intensities in the nucleus upon TNF treatment (two-sided Student’s t-test -Log10 p > 1.5, Log2 fold change > 0.5 or < −0.5). f Heatmap of means of the 20 most strongly up- and downregulated z-scored protein intensities in the cytosol upon TNF treatment (two-sided Student’s t-test -Log10 p > 1.5, Log2 fold change > 3 or < −3). g Heatmap of z-scored phosphosite intensities that are significantly regulated upon TNF treatment in the membrane, nucleus, and cytosol (two-sided Student’s t-test FDR < 0.05). The profiles are color-coded according to their distance from the respective cluster center (red is close to the center, blue is further away from the center). h Fisher’s exact test of phosphosites significantly enriched in the nucleus, membrane (p < 0.001), and cytosol (p < 0.01). The red scale represents enrichment, while gray represents no enrichment. Source data are provided as source file.