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. 2021 Jan 11;12:254. doi: 10.1038/s41467-020-20509-1

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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. 4 — a Experimental workflow for rhythmic ubiquitinome analysis. b Proportion of oscillating ubiquitination sites (q-value < 0.1) quantified in >50% of all samples (left panel, green) and proteins with cycling ubiquitin sites (q-value < 0.1) (right panel, violet) c Rose plots indicate phase peaks for cycling ubiquitination sites (left panel, green) and proteins (right panel, violet). d Overrepresentation analysis of gene ontology biological processes (GOBP) filtered for top 10 significant terms. Significance is determined by 5% false discovery rate (FDR) (Fisher’s Exact test). e Proportions of proteins with a single and multiple cycling ubiquitination sites (left panel) and those displaying cycling diGly site clusters (right panel). f, g Examples of proximity analysis of cycling ubiquitin clusters (http://cyclingubi.biochem.mpg.de). Cycling sites (q-value <0.1, ±SEM, n = 4 biologically independent experiments for each time point) (top) and their location in the protein sequence along with the domain annotation (middle) and proximity score (average distance, p-value < 0.1) (bottom) for f SLC7A11 (p-value = 0.0161) and g MAGED1 (p-value = 0.0863). Source data are provided as a Source data file.