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.