Examples of Gavin Benchmark Complexes Missed and Hit by MCODE Figure legend: Protein complexes are represented as graphs using the spoke model. Vertices represent proteins and edges represent experimentally determined interactions. Blue vertices are baits in the Gavin et al. study. A) A Cdc3 complex hand-annotated by Gavin et al. that was missed by MCODE because of a lack of connectivity information among sub-components. This complex annotation was the result of a single co-immunoprecipitation experiment. B) The Arp2/3 complex as annotated by Gavin et al. and as found by MCODE with parameters optimized to the data set. Note the five extra proteins that have minimal connectivity to main cluster. C) The protein connection map seen from the crystal structure of the Arp2/3 complex. The crystal structure is from Bos taurus (cow), but is assumed to be very similar to yeast based on very high similarity between cow and yeast Arp2/3 subunits.