Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis

Table 1 Predicted regulatory interactions

TF	Target	z-score	TFBS conservation	Ind. Ev.
LexA	cho	9.45	68.6%	[12, 16]
	dinB	8.38		[12, 16]
	dinI	9.84		[12, 16]
	dinD	7.69		[12, 16]
	yebG	10.39		[12, 16]
Fis	rplM ^$	-	15.1%	-
	rpsI	6.59
PdhR	lipA	9.42	72.9%	this study
PhoP	cysB	7.6	21.7%	-
KdgR	edd	8.92	0%	-

Overview over the regulatory interactions inferred by the use of DTI and validated through a phylogenetically conserved TFBS in the promoter region of the target gene not yet reported in RegulonDB. A total of 10 interactions of which five have already been reported elsewhere are predicted (indicated in column five). Of the 44 interactions that have been not included in Regulon DB v. 6.1 but have been validated through the search for a phylogenetically conserved binding site of the regulator, ten were ascertained through a functional relationship of the putative target with other known targets of the regulator. In the third column the z-score of the interaction and in the forth column the average overlap of known TFBS of the regulator with conserved regions of the genome are given. The interaction marked with ^$ lies within the same operon like a gene for which an interaction has been inferred. For additional interactions validated through the chromosomal location of the target downstream of an operon known to be regulated by the putative regulator see Additional File 1: Supplemental Material S8.

ISSN: 1752-0509