Extended Data Fig. 3: DVP discovers uncharacterized proteins with potential clinical relevance.

a, Violin plots showing nuclear area in pixels of the 6 nuclei classes identified by ML. b, Nuclear area in pixels of U2OS FUCCI cells in relation to the cell cycle pseudotime¹⁴. Color code indicates point density. c, Nuclear area of three major cell cycle states G1, G1/S and S/G2 determined by fluorescently tagged CDT1 and GMNN intensities and Gaussian clustering. Box plots show the results of n = 238,675 cells in total (85,551 for G1, 83,121 for G1/S and 70,003 for S/G2). d, Relative protein levels of all identified ORF proteins in the dataset. C7orf50, C1orf112, C19orf53 and C11orf98 were differentially expressed (ANOVA p-value < 0.05) across the 5 nuclei classes (n = 3 biological replicates). e, Mean intensities of immunofluorescent stained C7orf50 and the cell cycle markers ANLN and CCNB1 in U20S cells. C7orf50 levels were quantified in nuclei with low and high ANLN and CNNB1 intensities. Box plots show the results of n = 263 cells per condition (C7orf50-ANLN) and n = 412 per condition (C7orf50-CCNB1). f, Upper panel: Representative immunofluorescence images of C7orf50 and DNA (DAPI) stained U2OS cells¹⁹. Scale bar is 20 µm. Note, C7orf50 is enriched in nucleoli. Lower panel: Immunohistochemistry of a C7orf50 stained pancreatic adenocarcinoma (https://bit.ly/2X4re05). Image credit: Human Protein Atlas. Scale bar is 40µm. g, Kaplan-Meier survival analysis of pancreatic adenocarcinoma (https://bit.ly/3BAxewA) based on relative C7orf50 RNA levels (FPKM, number of Fragments Per Kilobase of exon per Million reads). RNA-seq data is reported as median FPKM, generated by The Cancer Genome Atlas (https://bit.ly/3iSOG8d). Patients were divided into two groups based on C7orf50 levels with n=41 low and n=135 high patients. A log-rank test was calculated with p = 0.0001. h, String interactome analysis for C7orf50. A high confidence score of 0.7 was used with the five closest interactors highlighted by color⁵⁴. The box plots in c and e define the range of the data (whiskers), 25th and 75th percentiles (box), and medians (solid line). Outliers are plotted as individual dots outside the whiskers.