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. 2019 Dec 4;10:5518. doi: 10.1038/s41467-019-13520-8

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© The Author(s) 2019

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. 2 — a, b SILAC profiles of host proteins infected with Pan (a) or Mal (b) compared to mock infection. The top 2% of proteins that are strongest produced during the last time period are highlighted. c Functional protein clusters least affected by host shutoff were identified. The 2% proteins with the highest ratios were selected for each time period and multi-list GO enrichment was performed. d Median, 25th, and 75th percentile of proteins related to a selected set of GO terms are highlighted in the direct SILAC comparison Pan/Mal. All other protein profiles in black. e Spearman’s rank correlation coefficients when comparing the indicated RNA and protein level data. f, g Scatterplot of mRNA changes vs. protein synthesis level changes in Pan/mock or Mal/mock infection conditions. Blue and orange coloring of data points reflects the density of data points. h Protein synthesis efficiencies calculated from absolute mRNA (RPKM, 8 hpi) and protein data (iBAQ, 8–12 hpi) (center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range, outliers (data points outside the whiskers) were removed for visibility). For the assessment of statistical significance two-sided Wilcoxon’s rank-sum tests were performed and p values are given (ns: non-significant). All data are based on the mean of n = 2 biological replicates.