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GSE67402: E.coli regulatory changes under long-term starvation

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Results for NarL

Z-value: 0.68

Transcription factors associated with NarL

Gene Symbol Gene ID Gene Info
narL
narL NarL

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
narL-0.281.6e-01Click!

Activity profile of NarL motif

Sorted Z-values of NarL motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
ompW 5.64
ompW
outer membrane protein W
hybOABCDEFG 4.18
hybG
hybF
hybE
hybD
hybC
hybB
hybA
hybO
hydrogenase 2 accessory protein
protein involved with the maturation of hydrogenases 1 and 2
hydrogenase 2-specific chaperone
predicted maturation peptidase for hydrogenase 2
hydrogenase 2, large subunit
hydrogenase 2 - integral membrane subunit HybB
hydrogenase 2 - [Fe-S] binding, ferredoxin-type component HybA
hydrogenase 2, small subunit
narK 4.09
narK
nitrate:nitrite antiporter NarK
ytfE 3.85
ytfE
iron-sulfur cluster repair protein YtfE
fdnGHI 3.08
fdnH
fdnI
fdnG
formate dehydrogenase N, β subunit
formate dehydrogenase N, γ subunit
formate dehydrogenase N, α subunit
dmsABC 2.97
dmsA
dmsB
dmsC
dimethyl sulfoxide reductase, chain A
dimethyl sulfoxide reductase, chain B
dimethyl sulfoxide reductase, chain C
dcuB-fumB 2.96
fumB
dcuB
fumarase B
dicarboxylate transporter DcuB
torCAD 2.92
torD
torA
torC
chaperone protein for trimethylamine-N-oxide oxidoreductase I
trimethylamine N-oxide reductase, catalytic subunit
trimethylamine N-oxide reductase, cytochrome c-type subunit
yeaR-yoaG 2.66
yoaG
yeaR
predicted protein
conserved protein
narGHJI 2.38
narG
narI
narH
narJ
nitrate reductase A, α subunit
nitrate reductase A, γ subunit
nitrate reductase A, β subunit
molybdenum cofactor assembly chaperone subunit (δ subunit) of nitrate reductase 1
citCDEFXG 2.11
citX
citC
citD
citE
citF
citG
apo-citrate lyase phosphoribosyl-dephospho-CoA transferase
citrate lyase synthetase
citrate lyase, acyl carrier γ subunit
citrate lyase, citryl-ACP lyase β subunit
citrate lyase, citrate-ACP transferase α subunit
triphosphoribosyl-dephospho-CoA synthase
caiF 1.79
caiF
CaiF transcriptional activator
hcp-hcr 1.79
hcr
hcp
NADH oxidoreductase
hybrid-cluster protein
dcuSR 1.47
dcuR
dcuS
DcuR transcriptional activator
DcuS sensory histidine kinase
hyaABCDEF 1.37
hyaB
hyaC
hyaA
hyaF
hyaD
hyaE
hydrogenase 1, large subunit
hydrogenase 1, b-type cytochrome subunit
hydrogenase 1, small subunit
protein involved in nickel incorporation into hydrogenase 1 proteins
protein involved in processing of HyaA and HyaB proteins
protein involved in quality control of HyaA
dpiBA 1.11
dpiB
dpiA
DpiB sensory histidine kinase
DpiA transcriptional dual regulator
napFDAGHBC-ccmABCDEFGH 1.02
napG
napF
napD
napC
ccmH
napA
ccmE
ccmD
ccmG
ccmF
ccmA
ccmC
ccmB
napH
napB
ferredoxin-type protein
ferredoxin-type protein
signal peptide-binding chaperone for NapA
periplasmic nitrate reductase, cytochrome c protein
holocytochrome c synthetase - thiol:disulfide oxidoreductase CcmH
large subunit of periplasmic nitrate reductase, molybdoprotein
membrane anchored periplasmic heme chaperone CcmE
ABC complex for formation and release of holoCcmE - membrane subunit CcmD
holocytochrome c synthetase - thiol:disulfide oxidoreductase CcmG
holocytochrome c synthetase - CcmF subunit
ABC complex for formation and release of holoCcmE - ATP binding subunit
ABC complex for formation and release of holoCcmE - membrane subunit CcmC
ABC complex for formation and release of holoCcmE - membrane subunit CcmB
ferredoxin-type protein
subunit of periplasmic nitrate reductase, cytochrome c550 protein
ydhYVWXUT 1.01
ydhY
ydhX
ydhW
ydhV
ydhU
ydhT
predicted 4Fe-4S ferredoxin-type protein
predicted 4Fe-4S ferredoxin-type protein
predicted protein
predicted oxidoreductase
predicted cytochrome
conserved protein
frdABCD 0.88
frdA
frdB
frdC
frdD
fumarate reductase flavoprotein
fumarate reductase iron-sulfur protein
fumarate reductase membrane protein
fumarate reductase membrane protein
nikABCDER 0.44
nikB
nikC
nikA
nikD
nikE
nikR
nickel ABC transporter - membrane subunit
nickel ABC transporter - membrane subunit
nickel ABC transporter - periplasmic binding protein
nickel ABC transporter - ATP binding subunit
nickel ABC transporter - ATP binding subunit
NikR DNA-binding transcriptional repressor, Ni-binding
norVW 0.34
norW
norV
NADH:flavorubredoxin reductase
flavorubredoxin
ydeP 0.20
ydeP
acid resistance protein
nrfABCDEFG 0.08
nrfF
nrfG
nrfD
nrfE
nrfB
nrfC
nrfA
activator of formate-dependent nitrite reductase complex
NrfG
formate dependent nitrite reductase - NrfD subunit
formate-dependent nitrite reductase; possible assembly function
formate-dependent nitrite reductase - penta-heme cytochrome c
formate-dependent nitrite reductase, 4Fe-4S subunit
formate dependent nitrite reductase - NrfA subunit

Network of associatons between targets according to the STRING database.

First level regulatory network of NarL

PNG image of the network

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

Log-likelihood per target  Total log-likelihood Term Description
1.4 4.2 GO:0019563 glycerol catabolic process(GO:0019563)
1.0 3.9 GO:0030091 protein repair(GO:0030091)
0.9 4.5 GO:2001057 reactive nitrogen species metabolic process(GO:2001057)
0.8 2.3 GO:0015707 nitrite transport(GO:0015707)
0.6 13.8 GO:0009061 anaerobic respiration(GO:0009061)
0.6 1.8 GO:0009437 carnitine metabolic process(GO:0009437)
0.4 1.1 GO:0071310 cellular response to organic substance(GO:0071310)
0.3 2.1 GO:0018209 peptidyl-serine modification(GO:0018209)
0.1 1.5 GO:0006468 protein phosphorylation(GO:0006468)
0.1 0.4 GO:0006935 chemotaxis(GO:0006935) taxis(GO:0042330)
0.0 0.2 GO:0010447 response to acidic pH(GO:0010447)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
2.4 2.4 GO:0031235 intrinsic component of the cytoplasmic side of the plasma membrane(GO:0031235)
1.4 9.5 GO:0098567 periplasmic side of plasma membrane(GO:0098567)
0.3 0.9 GO:0045273 respiratory chain complex II(GO:0045273) plasma membrane respiratory chain complex II(GO:0045274)
0.3 3.1 GO:0031233 intrinsic component of external side of plasma membrane(GO:0031233)
0.1 5.6 GO:0044462 cell outer membrane(GO:0009279) external encapsulating structure part(GO:0044462)
0.1 4.4 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.4 1.4 GO:0005048 signal sequence binding(GO:0005048)
1.2 2.4 GO:0008940 nitrate reductase activity(GO:0008940)
0.9 5.6 GO:0030151 molybdenum ion binding(GO:0030151)
0.8 4.2 GO:1902670 carbon dioxide binding(GO:1902670)
0.8 2.3 GO:0015113 nitrite transmembrane transporter activity(GO:0015113)
0.7 2.1 GO:0051192 prosthetic group binding(GO:0051192)
0.6 3.0 GO:0004333 fumarate hydratase activity(GO:0004333)
0.3 0.9 GO:0000104 succinate dehydrogenase activity(GO:0000104) oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor(GO:0016635)
0.3 2.2 GO:0016661 oxidoreductase activity, acting on other nitrogenous compounds as donors(GO:0016661)
0.3 3.0 GO:0009055 electron carrier activity(GO:0009055)
0.2 1.1 GO:0000156 phosphorelay response regulator activity(GO:0000156)
0.2 1.5 GO:0001140 transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding(GO:0001140)
0.1 0.4 GO:0015099 nickel cation transmembrane transporter activity(GO:0015099)
0.1 3.9 GO:0005506 iron ion binding(GO:0005506)
0.0 1.8 GO:0003700 transcription factor activity, sequence-specific DNA binding(GO:0003700)