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Table 2 Interactions predicted by C3NET, shown as red edges in Fig. 7, declared as false positives according to the reference network G 2007 E C .

From: Inferring the conservative causal core of gene regulatory networks

 

regulator gene

regulated gene

literature

confirmed

gadE

gadB

[49]

 

gadE

hdeD

[49]

 

gadE

yhiD

[50]

 

lrp

pntA

[51]

 

fliA

tsr

[52]

 

flhD

flhC

[53] (protein complex)

predicted interactions

dnaA

amiB

 
 

dnaA

rnpA

 
 

fliA

flgA

 
 

lrp

artJ

 
 

lrp

aroP

indirect interaction via TyrR [47]

 

lexA

araB

 
 

lexA

araD

 
 

lexA

araE

 
 

lrp

pntB

 
 

tdcR

yiaM

 
 

tdcR

bglG

 
 

csgD

trpD

 
 

csgD

trpC

 
 

zur

glmU

 
 

purR

aroH

 
 

fnr

dinF

 
 

cbl

treB

 
 

gadE

slp

 
 

gadE

dps

 
  1. Among these 25 interactions 6 receive support from the literature to be in fact true positives.