Fig. 4

Predicting complexes (Complexes.m). a. 2311 co-fractionation profiles from a single replicate of D1, sorted by peak location. Fourteen 20S proteasomal proteins group together (protein numbers 851–864). b. Square connection matrix for same proteins as (a). Colour shows interaction score for all 19,740 interactions with score greater than 0.50. Inset: Close up of the 14 × 14 connection matrix for 20S proteasomal members plus other proteins (protein numbers 851–865). c. Co-fractionation profiles for the 14 proteins from B inset, which also correspond to a predicted complex. Profiles of complex members (left) all have a similar shape. When compared to its closest match in CORUM, the 20S proteasome, this predicted complex had 13 overlapping proteins (purple), as well as one protein in the predicted complex that was not in the 20S proteasome (orange). Additionally, there was a single protein from the 20S proteasome that was not in the predicted complex (black). d. Example predicted complex with no match in the CORUM database. e. Force diagrams for all 71 predicted complexes from 19,740 interactions in D1. Same colouring scheme as (d and e). Proteins in known complexes that were not predicted (i.e. Reference-only, black) are omitted for clarity. f. Predicted complexes are composed of known (“recovered”) subunits and novel subunits. Data is from all four datasets. The size of each predicted complex is the sum of novel and recovered members