Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

Table 2 Valid search of 12 predicted new links using literature.

TF	Gene	Supporting Evidence
DicA	insD	TF binding site verified (RegulonDB) [34]
DicA	intQ	TF binding site verified (RegulonDB) [34]
DicA	ydfE	TF binding site verified (RegulonDB) [34]
DcuR	pepE	Involved in anaerobic respiration related process (EcoCyc [37])
Fur	ybdB	ybdB (entH) is proposed to be regulated by Fur (EcoCyc [37])
Fur	yncE	yncE is de-repressed by Fur [41]
IscR	fdx	Some evidence that the Fdx functions as an intermediate site for Fe-S cluster assembly [42]
IscR	hscA	HscA is required for the assembly of Fe-S clusters [43, 44]
IscR	hscB	HscB is a co-chaperone that stimulates HscA (Hsc66) ATPase activity [44]
IscR	iscX	Possibly involved in Fe-S cluster biogenesis [43]
SgrR	sroA	TF binding site verified (RegulonDB)[34]

New regulatory links of E. coli predicted in a reconstructed gene regulatory network of size of 200 links (includes 16 potential new regulatory links).

ISSN: 1471-2105