Extended Data Fig. 5: Captured modules comparison for BIONIC and input networks for optimal clustering parameters.

Known protein complexes (as defined by the IntAct standard) captured by individual networks and the unsupervised BIONIC integration of these networks (denoted BIONIC). Hierarchical clustering was performed on the datasets and resulting clusters were compared to known IntAct complexes and scored for set overlap using the Jaccard score (ranging from 0 to 1). The clustering algorithm parameters were optimized for each module individually, unlike the analysis in Fig. 2 where the clustering parameters were optimized for the standard as a whole. Each point is a protein complex, as in Fig. 2c. The dashed line indicates instances where the given data sets achieve the same score for a given module. Histograms indicate the distribution of overlap (Jaccard) scores for the given dataset, and the labelled dashed line indicates the mean of this distribution. The individual modules shown here as well as for the KEGG Pathways and IntAct Complexes module standards can be found in Supplementary Data File 4. The LSM2-7 complex is indicated by the arrows. PPI = protein-protein interaction. This analysis uses the same networks and BiONIC features as Fig. 2.