m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence

Table 1 Summary of comparison with similar methods

Method	Software	Reference	ΔTF expression	TFBS	Gene function	Nucleosomes
Univariate multinomial regression	m:Explorer		Discretized	Discretized	Discretized	Discretized
Multivariate multinomial regression			Discretized	Discretized	Discretized	Discretized
Decision tree	GeneClass	[15]	Discretized	Discretized	Discretized
Kolmogorov Smirnov test		[10]		Discretized	Numeric¹
Mutual information	ARACNE	[11]	Numeric		Discretized⁴
Fisher's exact test			Discretized³	Discretized³	Discretized	Discretized³
Biclustering	SAMBA	[13]	Discretized	Discretized	Discretized⁴	Discretized
Univariate linear regression	REDUCE	[14]		Numeric²	Numeric¹
Multivariate linear regression	REDUCE	[14]		Numeric²	Numeric¹

1. Gene expression values from cell cycle time-course. 2. Promoter sequence data and TF-DNA binding affinity matrices. 3. TF target genes treated as union of gene expression and TFBS targets. 4. Fisher's test used for finding cell cycle TFs in constructed network or clustering. TF, transcription factor knockout strain; TFBS, transcription factor binding site.

ISSN: 1474-760X