Fig. 3
Generation of comprehensive interactome maps for the bona fide cellular markers. The 18 localization markers we subjected to our integrated analysis, resulting in identification of 679 HCIs from the AP-MS and 2118 HCIs from BioID analysis. a The distribution of the number of known (blue) and newly identified (red) interactions within 18 bona fide subcellular organelle/structure markers, illustrate the need for systematic analyses. b The distribution of the number of interactions per localization marker by AP-MS or BioID purification approach shows similar distribution of connectivity as other publications using these approaches individually. Boxplots show the median, the 25th and 75th percentile, Tukey whiskers (median ± 1.5IQR). c, d The protein-protein interaction network and molecular context for proteasome organelle marker (PSA1) and nuclear envelope (LMNA). The HCIs that were identified from AP-MS (green line) and BioID (yellow line) are shown together with the known prey-prey interactions (dashed gray line). The nodes are color-coded based on the localization rank obtained from the CellWhere database (key: dark green = primary cellular localization for the corresponding protein, light green = possible localization, gray = different or no localization assigned for the protein). The Venn diagram highlights the complementary nature of the AP-MS and BioID approaches. e The reference molecular context map for the 18 subcellular organelles/structures. The unique high-confidence interactors from the BioID analysis are arranged in a circle around the corresponding localization marker and the shared interactors are shown with corresponding colors representing multiple localizations. Preys with more than four subcellular localizations are shown in gray color. The newly identified interactions are shown in pink edges and the known interactions with blue
