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

BMC Bioinformatics

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

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

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.

ISSN: 1471-2105