Table 3. Relationships between parameters of clustering and biological enrichment.

Metric		Top Quartile	Bottom Quartile
F	K		6
	transform	FFT, center
	distance	chebychev	cityblock
	algorithm		Kmeans
C	K
	transform	FFT,center
	distance	euclidean	cityblock
	algorithm	SOM	Kmeans
P	K		6, 8
	transform	FFT, center	log10, nMaxLog10, rangeScale
	distance
	algorithm	AP	Kmeans
PFAM	K	12, 14
	transform	pow	zscore, rangeScale
	distance	cityblock
	algorithm		Kmeans, SOM
Motifs	K	6	10
	transform	log10, normMax	zscore
	distance
	algorithm	Ncut
Scansite Bind	K	6	14
	transform	nMaxLog10
	distance
	algorithm		Kmeans, Ncut
Scansite Kinase	K	12	6
	transform	FFT
	distance
	algorithm

Parameters are given for each biological metric if they are enriched in either the top or bottom quartile of the list when ranked by the number of labels enriched in that category. PELM kinase annotations and Pfam_site did not perform better than random controls, and are not included. Although Scansite Kinase parameter enrichment also did not perform better than random controls, it is listed here since subsets based on the FFT did perform better than their random control counterparts. See Table 2 for a full description of parameters.