Incorporating time-delays in S-System model for reverse engineering genetic networks

BMC Bioinformatics

Table 11 “True”+“Novel” interactions of E. coli network inferred by TDSS and other state-of-the-art methods

	Considering 6-gene subnetwork					Considering 8-gene subnetwork
True	Proposed	REGARD	S-Tree	NGnet	Kimura	Proposed	ALG	Perrin	BANJO	GlobalMIT	BITGRN2
positives	(TDSS)	[19]	[39]	[46]	et al[53]	(TDSS)	[34]	et al[47]	[43]	[23]	[24]
lexA⊣recA	√	√	√	√	⋆	√	√	√		√	√
lexA⊣lexA	√	√	√	√	⋆	√	√	√
lexA⊣umuD	√	√	√	√	⋆	√	√			√	√
lexA⊣uvrD	√	√		√	⋆	√	√				√
lexA⊣uvrA	√	√	√		⋆	√	√	√	√	√	√
lexA⊣polB	√		√	√	⋆	√				√
recA→lexA			√	⋆	⋆		√	√	√
lexA⊣uvrY						√				√
lexA⊣ruvA
Total TP inferred	6	5	6	5	0	7	6	4	2	5	4
Novel Interactions
umuD→lexA	√	√			⋆	√	√	√		√
uvrA⊣lexA	√	√		⋆	√	√		√
uvrA⊣recA			√	⋆	⋆			√	√	√
Total Novel Interactions	2	2	1	0	1	2	1	3	1	2	0

ISSN: 1471-2105