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.

Reimand et al. Genome Biology 2012 13:R55   doi:10.1186/gb-2012-13-6-r55

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