Extended Data Fig. 3: Fusing protein distances from immunofluorescence and affinity purification.

a, b, Protein pairs ranked by similarity in AP–MS embedding enrich for the most similar protein pairs in IF (a), and vice versa (b). c, Calibrating physical diameter, D, of subcellular components against the number of proteins, C, assigned to the corresponding Gene Ontology (GO) terms. d, Supervised model (random forest) estimates physical proximity (nm) of all pairs of proteins from their IF and AP–MS embeddings. e, Performance of model in recovering protein-protein distances in GO in five-fold cross validation (red, Pearson’s r). Equivalent calculation for random feature sets (grey). Statistics calculated using two-sided paired t-test. Data are presented as mean values +/- standard deviation.