Table 3 The transcriptional regulatory network used in this study for the 100 responsive genes in E. coli when subjected to carbon source transition from glucose to acetate media.

AceA

-ArcA, -FruR, -IclR, +IHF

ldcC

+RpoS

trpA

-TrpR

AceB

-ArcA, -FruR, -IclR, +IHF

leuA

+LeuO

trpC

-TrpR

AceK

-ArcA, -FruR, -IclR, +IHF

leuB

+LeuO

tyrA

-TyrR

Acs

+Crp, +IclR, +RpoS, +FNR

leuC

+LeuO

tyrR

-TyrR

AdhE

-FruR, -NarL, +RpoS, +FIS

livJ

-Lrp,

ugpB

+Crp, +PhoB

aidB

+RpoS, +ada

livK

+FruR, -Lrp

ugpE

+Crp, +PhoB

arcA

+ArcA, +FNR

lrp

-Lrp, +RpoS, +GadE

uspA

-FadR

aroF

-TyrR

mdh

-ArcA, +Crp, -FlhD

wrbA

+RpoS

aroG

-TyrR

mdoH

+RpoE

xthA

+RpoS

aroM

-TrpR, -TyrR

mutH

+RpoS

yciG

+RpoS

aroP

-TyrR

narH

+NarL, +IHF, +FNR

csgD

+CsgD, +OmpR

narl

+NarL, +IHF, +FNR

csgE

+CsgD, +OmpR

narY

+RpoS

csgF

+CsgD, +OmpR

nrfE

+NarL

csiE

+Crp, +RpoS, +HNS

nuoA

-ArcA, +NarL, -IHF, -FNR

cyoA

-ArcA, -FNR

nuoE

-ArcA, +NarL, -IHF, -FNR

cyoB

-ArcA, -FNR

nuoF

-ArcA, +NarL, -IHF, -FNR

cysA

+CysB

nuoH

-ArcA, +NarL, -IHF, -FNR

cysH

+CysB

nuoJ

-ArcA, +NarL, -IHF, -FNR

cysK

+CysB

osmE

-IHF

cysM

+CysB

phoR

+PhoB, +TrpR

dapA

+ RpoE

poxB

+RpoS, +MarA, +SoxS

Epd

+Crp, +FruR

ppsA

+FruR

fabA

+FadR

prop

+Crp, +RpoS, +FIS

FtsZ

+RpoS, +SdiA, +RcsA

pspA

+IHF, +PspF, +RpoN

gale

+Crp, -GalR, -Rob

pstC

+PhoB

galK

+Crp, -GalR, -Rob

pstS

+PhoB

galT

+Crp, -GalR, -Rob

purA

+RpoE

gatA

-GatR

purK

-PurR

gatC

-GatR

purM

-PurR

gatD

-GatR

pykF

-FruR

gatY

-GatR, +LeuO

rfaF

+RpoE

glgA

+Crp

rob

+RpoS

glgP

+Crp

rpoD

+RpoE, -Lexa

glgS

+Crp

rpoE

+RpoE

glpD

+Crp, -GlpR

rseC

+RpoE

gltA

-ArcA, +Crp

sdhA

-ArcA, +Crp, -FNR, -FIS

Gor

+OxyR

sdhB

-ArcA, +Crp, +NarL, -FNR, -FIS

guaB

-PurR

serA

+Lrp

hdeA

+RpoS, +GadX, +GadE

sucB

-ArcA, +Crp, -FNR, -FIS

hdeB

+RpoS, +GadX, +GadE

sucC

-ArcA, +Crp, -FNR, -FIS

IclR

-FadR

sucD

-ArcA, +Crp, -FNR, -FIS

IlvB

+Crp

surA

+RpoE

ilvH

+Lrp

tnaL

CAP

Kbl

+Lrp

topA

+FIS