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. 2023 Nov 3;14:7034. doi: 10.1038/s41467-023-42822-1

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© The Author(s) 2023

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 Schematic of enrichment procedure for ubiquitinated proteins using the diglycine antibody, which targets the GG remnants of ubiquitinated regions following trypsin digestion. Created with BioRender.com. b Volcano plot showing the distribution of proteins in the whole proteome analysis of Appl deleted flies. Protein level changes greater than 1.25-fold are indicated as pink and violet dots. Violet dots indicate upregulated proteins; pink dots indicate down-regulated proteins. The grey line marks False Discovery Rate (FDR) adjusted two-tailed p-value = 0.05. Proteins indicated by dots below that line are not considered statistically significant. c Volcano plot showing the distribution of ubiquitinated proteins in Appl deleted flies. DiGlycine peptide changes, indicating ubiquitination, above 1.25-fold, are indicated as pink and violet dots. Violet dots indicate upregulated proteins; pink dots indicate down-regulated proteins. The grey line marks False Discovery Rate (FDR) adjusted two-tailed p-value = 0.05. Proteins indicated by dots below that line are not considered statistically significant. d Protein networks altered by removing Appl. Louvain clustering of proteins altered in proteome and ubiquitinome analysis of flies without Appl show enrichment of proteostasis-related networks such as translation, protein folding, and ubiquitin-dependent degradation. Shapes of the nodes show the source of protein. Steiner nodes are the proteins that are not experimentally altered; however, they are predicted to be associated with loss of Appl. Results from single-cell RNA sequencing data were used to adjust edge confidence and node weights in the network. The cost of the edges is determined by the confidence in the protein-protein interaction as calculated by STRING. These edges were weighted by the number of single cell clusters with altered candidate gene expression. A lower cost indicates greater confidence in the protein-protein interaction. Source data are provided as a Source Data file.