Table II.

Benchmarking of cluster qualities

The size and composition of expert-curated Arabidopsis families collected from literature (Reference column) is compared to results obtained with HCL and BCL. The last example represents a family of unknown function for which no Pfam domain or references are available. The provided numbers represent the family sizes, while several numbers in a field indicate the size of the obtained subfamilies in decreasing order. Only one gene/protein model was counted per gene. The number “1” stands for singlet (e.g. “5 × 1” stands for five singlets). Data sources are provided as footnotes. *, These counts do not include truncated genes or those that are absent in the latest genome annotation. n.a., Not available.

Family Name	Reference	HCL	BCL
Cytochrome P450 familya	244	239/5×1	151/31/28/19/4/3/8×1
Acyl-group desaturasesb	15	15	9/4/1/1
Stearoyl-ACP desaturasesb	7	7	7
Xyloglucan xylosyltransferasesc	7*	7	7
Xyloglucan fucosyltransferasesd	9*	9	9
Phototropinse	2	2	2
Auxin response factorsf	23	17/6	20/3×1
Fatty acid multifunctional proteinsg	2	2	2
Phospholipase D familyh	12*	9/3×1	10/2
Δ8 sphingolipid desaturasesi	2	2	2
Nitrate reductasesj	2	2	2
Expressed protein (BCL ID: 321)	n.a.	10×1	10

^aNelson et al. (2004).

^bBeisson et al. (2003).

^cFaik et al. (2002).

^dSarria et al. (2001).

^eBriggs and Christie (2002).

^fOkushima et al. (2005).

^gRichmond and Bleecker (1999).

^hQin and Wang (2002).

ⁱSperling et al. (1998).

^jWang et al. (2004).