Fig. 4: Identifying the interactors of the Usp10-rin recycling complex.

a A dual volcano plot showing the log2 of fold changes and -log10 of FDR of proteins in Control (MHC-Gal4 > w-) vs. Usp10 OE (MHC-Gal4>Usp10 OE; the top half part) and Control (MHC-Gal4 > w-) vs. rin OE (MHC-Gal4>rin OE; the bottom half part) comparisons. Significantly upregulated (red) and downregulated (blue) genes are shown as colored dots. Significantly upregulated and downregulated mitochondrial genes are shown as green dots. The statistical significance threshold was FDR < 0.05, and the normalized ratio threshold was |log2(FC)| > 0.323. b A dual volcano plot showing the log2 of fold changes and -log10 of FDR of proteins in Control (MHC-Gal4 > w-) vs. Usp10 RNAi (MHC-Gal4>Usp10-shRNA; the top half part) and Control (MHC-Gal4 > w-) vs. rin RNAi (MHC-Gal4>rin RNAi-2; the bottom half part) comparisons. Significantly upregulated (red) and downregulated (blue) genes are shown as colored dots. The statistical significance threshold was FDR < 0.05, and the normalized ratio threshold was |log2(FC)| > 0.323. c, d Bubble plots showing the significant pathways from the pairwise Gene Set Enrichment Analysis (GSEA) comparison in Usp10 OE and rin OE groups. The vertical axis represents the pathway names, and the horizontal axis represents the normalized enrichment score. Pathways are ranked by their FDR from top to bottom. The FDR is depicted by the color of dots. A lower FDR value corresponds to a color closer to red, while a higher FDR value corresponds to a color closer to blue; gray indicates a lack of significance in the FDR value but ranks highly in the GSEA. The number of differentially expressed genes included in each pathway is illustrated by the size of the bubbles. e–g Heatmaps of gene sets (pathways) for “Regulation of TP53 activity” (e), “mTOR signaling” (f), and “Macroautophagy/Autophagy” (g), containing the expression levels of enriched genes in Control and Usp10 OE samples. The colors range from dark red to dark blue, representing the highest and lowest expression of genes, respectively. Source data are provided in the Supplementary Data files.