Extended Data Fig. 5: Supporting analyses for PRRPA.
From: A multi-scale map of cell structure fusing protein images and interactions
a, Distributions of protein-protein distance z-scores among the seven proteins in the PRRPA system for IF (top, red) or AP–MS (bottom, blue) modalities, calibrated to all such distances, respectively (grey). Statistics calculated using one-sided Mann–Whitney U test. b, Specific recovery of new AP–MS interactions within PRRPA is shown (dark blue bar), in comparison to interactions between proteins in PRRPA and other proteins organized under the same parent systems (“Ribosome” and “Ribosome biogenesis assembly”, light blue bar), or between proteins in PRRPA and those organized elsewhere in MuSIC (grey bar). c, Mature 28S/18S rRNA ratio under siRNAs targeting each PRRPA protein (green) versus scrambled siRNA (grey), n = 3 biological replicates. FDR from two-sided t-test with Benjamini–Hochberg correction. Data are presented as mean values +/- standard deviation. d–i, Western blot analysis (d, e, Simple western assay; f–i, SDS–PAGE) of target protein abundance after treating HEK293T cells with respective siRNA for 72 h (Supplementary Tables 6, 7). The siRNAs highlighted in red were selected to assess the perturbation of mature rRNA ratio (28S/18S rRNA) when knocking down target protein, with protein knockdown efficiency confirmed using western blot in three additional biological replicates. For source data, see Supplementary Fig. 1 (gel; d–i) and Supplementary Fig. 2 (total RNA profiles; c).
