Unique, high-confidence, novel predicted yeast complexes. (a) Number of complexes predicted and number of proteins covered. (b) Semantic coherence of predicted complexes. (a) Number of yeast complexes predicted and number of proteins covered, using the five weighting approaches and the COMBINED clustering strategy. SWC generates more novel complexes that cover a greater number of proteins. (b) BP, CC, and MF semantic coherence of the predicted complexes and the reference complexes CYC2008. SWC's complexes have higher BP and CC coherence compared to the other weighting approaches (p < 0.05) except for NOWEI (for which there were too few predictions to obtain a significant p-value), but lower BP and CC coherence compared to the CYC2008 complexes. The MF coherence for SWC, STRING, BOOST, and CYC2008 complexes are similar, and are higher than that of TOPO or NOWEI (p < 0: 0005).