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Table 1 Summary of MCODE Results with Best Parameters on Various Data Sets.

From: An automated method for finding molecular complexes in large protein interaction networks

Data Set Number of Proteins Number of Interact-ions Number of Predicted Complexes MCODE Complexes Predicted Above ω = 0.2 Matched Benchmark Complexes Complex Benchmark Best MCODE Parameters
Gavin Spoke 1363 3225 82 63 88 Gavin hFfT\0.05\0.05
Gavin Spoke 1363 3225 53 20 20 MIPS hTfT\0.1\0.35
Pre HTMS 4379 9088 158 21 28 Gavin hTfT\0\0.2\
Pre HTMS 4379 9088 166 52 64 MIPS hTfT\0.1\0.2
AllYeast 4825 15143 209 52 76 Gavin hFfT\0\0.1
AllYeast 4825 15143 209 54 63 MIPS hTfT\0\0.1
AllYeast 4825 15143 203 80 150 MIPS+Gavin hTfT\0\0.15\
Benchmark 1762 3310 141 23 30 Gavin hTfT\0\0.3
Benchmark 1762 3310 163 58 67 MIPS hTfT\0.1\0.05
HTP Only 4557 12249 138 46 77 Gavin hTfT\0.05\0.1
HTP Only 4557 12249 122 29 35 MIPS hTfT\0.05\0.15
Y2H 3847 6133 73 7 7 Gavin hTfT\0.2\0.1
Y2H 3847 6133 78 21 26 MIPS hTfT\0\0.1
  1. Statistics and a summary of results are shown for the various data sets used to evaluate MCODE. 'Gavin Spoke' is the Gavin et al. data set represented as binary interactions using the spoke model; 'Pre HTMS' is the set of all yeast interaction not including the recent high-throughput mass spectrometry studies [6, 7].; 'AllYeast' is the set of all yeast interactions that we could collect; 'Benchmark' is a set of interactions found in the literature from YPD, MIPS and PreBIND; 'HTP Only' is the combination of all large-scale and high-throughput yeast two-hybrid and mass spectrometry data sets; 'Y2H' is the set of all yeast two-hybrid results from large-scale and literature sources. See Methods for full explanation of data sets. The 'Best MCODE Parameters' are formatted as haircut True of False, fluff True or False\VWP\Fluff Density Threshold Parameter.