Table 5

Comparison of function conservation approach with EEL algorithm

Function conservation

EEL algorithm

TFBS detection

Finding all potential TFBSs

Finding all potential TFBSs

Distance constraint used

Yes

Yes

Alignment technique used

None

Non-direct DNA sequence alignment

Distance between TFBSs

Any

Relatively close

Number of genes compared

Identification of conserved TFBSs at multiple gene level

Identification of conserved TFBSs at single gene level

Parameters used for predicting interacting TFs

Conserved TFBS with function conservation of TFs at multiple gene (genome scale) level

Conserved TFBS with TF binding affinity at single gene level

Sensitivity*

Higher

Lower

Specificity*

Higher

Lower

*Relative comparison results between the function conservation approach and EEL algorithm from this study.

Hu et al. Genome Biology 2007 8:R257   doi:10.1186/gb-2007-8-12-r257