Table 3.

Runtimes for each clustering method

	Small (3-10 genes)		Medium (11-100 genes)		Large (101-1000 genes)
Clustering Method	Param	Time (s)	Param	Time (s)	Param	Time (s)	Implementation
K-Clique Communities	0.80/03		0.80/57		0.80/48		Standalone,***
Maximal Clique	0.80	26.510	0.80	26.510	N/A	N/A	Standalone,***
Paraclique	0.80/01	5.120	0.80/09	0.780	0.60/09	9.050	Standalone,***
Ward (H)	N/A	2.863	N/A	2.863	N/A	2.863	R 2.13.0
CAST	0.875	37.324	0.85	34.242	0.90	34.121	MeV 4.5.1
QT Clust	030	6 904.518	035	6 759.073	050	5 559.467	MeV 4.5.1
Complete (H)	N/A	2.721	N/A	2.721	N/A	2.721	R 2.13.0
NNN	11	25.550	24	30.610	27	34.370	Standalone,***
K-Means	617	6 711.143	308	4 060.351	21	1 068.069	R 2.13.0
SOM	25/r	6.159	25/h	6.121	18/r	2.956	MeV 4.5.1
WGCNA	2/10	79.430	1/06	80.962	2/06	80.962	R 2.13.0
Average (H)	N/A	2.452	N/A	2.452	N/A	2.452	R 2.13.0
McQuitty (H)	N/A	2.445	N/A	2.445	N/A	2.445	R 2.13.0
CLICK	015	38.270	060	45.310	065	52.570	Standalone,***

Parameters used to produce the best Jaccard score, and the associated runtime for the given method and parameters are displayed. Specific parameter descriptions are listed in Table 1. MeV times were reported by GUI results. Hierarchical methods use the "flashClust" package for R, which is a C++ implementation of the standard "hclust" package. Hierarchical timings do not include the time for tree cutting (which is negligible). flashClust and WGCNA packages were downloaded from the CRAN repository June 22, 2011. Versions reported refer to the version used for runtime calculation; in some cases, previous versions were used to generate clusters for scoring. r = rectangular, h = hexagonal. *A GUI-based graphical tool which is no longer maintained was used to generate clusters for Jaccard scoring while the latest R implementation was using in timing, **Total elapsed time reported by the system.