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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for NarL

Z-value: 0.43

Transcription factors associated with NarL

Gene Symbol Gene ID Gene Info
narL
narL NarL

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
narL-0.393.4e-01Click!

Activity profile of NarL motif

Sorted Z-values of NarL motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
dmsABC 1.22
dmsA
dmsB
dmsC
dimethyl sulfoxide reductase, chain A
dimethyl sulfoxide reductase, chain B
dimethyl sulfoxide reductase, chain C
ynfEFGH-dmsD 1.05
ynfG
ynfF
ynfE
dmsD
ynfH
putative selenate reductase, predicted Fe-S subunit
putative selenate reductase, oxidoreductase subunit
putative selenate reductase, oxidoreductase subunit
DMS reductase maturation protein
putative selenate reductase, predicted membrane anchor subunit
adhE 1.01
adhE
aldehyde-alcohol dehydrogenase
ompW 0.78
ompW
outer membrane protein W
dcuB-fumB 0.69
fumB
dcuB
fumarase B
dicarboxylate transporter DcuB
hybOABCDEFG 0.67
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
nrfABCDEFG 0.57
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
frdABCD 0.55
frdA
frdB
frdC
frdD
fumarate reductase flavoprotein
fumarate reductase iron-sulfur protein
fumarate reductase membrane protein
fumarate reductase membrane protein
ydhYVWXUT 0.36
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
hcp-hcr 0.32
hcr
hcp
NADH oxidoreductase
hybrid-cluster protein
ytfE 0.24
ytfE
iron-sulfur cluster repair protein YtfE
dcuSR 0.19
dcuR
dcuS
DcuR transcriptional activator
DcuS sensory histidine kinase
aspA 0.17
aspA
aspartate ammonia-lyase
ydeP 0.16
ydeP
acid resistance protein
norVW 0.15
norW
norV
NADH:flavorubredoxin reductase
flavorubredoxin
aspA-dcuA 0.12
aspA
dcuA
aspartate ammonia-lyase
dicarboxylate transporter DcuA
caiF 0.11
caiF
CaiF transcriptional activator
nuoABCEFGHIJKLMN 0.07
nuoB
nuoC
nuoA
nuoF
nuoG
nuoE
nuoJ
nuoK
nuoH
nuoI
nuoN
nuoL
nuoM
NADH:ubiquinone oxidoreductase, chain B
NADH:ubiquinone oxidoreductase, chain CD
NADH:ubiquinone oxidoreductase, membrane subunit A
NADH:ubiquinone oxidoreductase, chain F
NADH:ubiquinone oxidoreductase, chain G
NADH:ubiquinone oxidoreductase, chain E
NADH:ubiquinone oxidoreductase, membrane subunit J
NADH:ubiquinone oxidoreductase, membrane subunit K
NADH:ubiquinone oxidoreductase, membrane subunit H
NADH:ubiquinone oxidoreductase, chain I
NADH:ubiquinone oxidoreductase, membrane subunit N
NADH:ubiquinone oxidoreductase, membrane subunit L
NADH:ubiquinone oxidoreductase, membrane subunit M
napFDAGHBC-ccmABCDEFGH 0.03
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
ubiCA 0.01
ubiC
ubiA
chorismate lyase
4-hydroxybenzoate octaprenyltransferase
nirBDC-cysG 0.01
nirD
cysG
nirC
nirB
nitrite reductase, small subunit
siroheme synthase subunit
nitrite transporter NirC
nitrite reductase, large 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
0.3 1.0 GO:0006067 ethanol metabolic process(GO:0006067)
0.2 1.2 GO:0006113 fermentation(GO:0006113)
0.2 0.6 GO:0018063 protein-heme linkage(GO:0017003) protein-tetrapyrrole linkage(GO:0017006) cytochrome c-heme linkage(GO:0018063)
0.2 0.5 GO:0046210 nitric oxide metabolic process(GO:0046209) nitric oxide catabolic process(GO:0046210)
0.1 0.8 GO:0015740 C4-dicarboxylate transport(GO:0015740)
0.1 0.2 GO:0030091 protein repair(GO:0030091)
0.0 0.1 GO:0009437 carnitine metabolic process(GO:0009437)
0.0 0.2 GO:0006531 aspartate metabolic process(GO:0006531)
0.0 0.1 GO:1902600 hydrogen ion transmembrane transport(GO:1902600)
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
0.3 1.9 GO:0098567 periplasmic side of plasma membrane(GO:0098567)
0.2 0.6 GO:0045274 respiratory chain complex II(GO:0045273) plasma membrane respiratory chain complex II(GO:0045274)
0.1 1.0 GO:0031234 extrinsic component of cytoplasmic side of plasma membrane(GO:0031234)
0.0 0.8 GO:0044462 cell outer membrane(GO:0009279) external encapsulating structure part(GO:0044462)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 0.8 GO:0005469 succinate:fumarate antiporter activity(GO:0005469)
0.2 0.6 GO:0016635 succinate dehydrogenase activity(GO:0000104) oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor(GO:0016635)
0.1 0.7 GO:1902670 carbon dioxide binding(GO:1902670)
0.1 0.5 GO:0016662 oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor(GO:0016662)
0.1 1.0 GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor(GO:0016620)
0.0 0.3 GO:0016684 peroxidase activity(GO:0004601) oxidoreductase activity, acting on peroxide as acceptor(GO:0016684)
0.0 1.3 GO:0016667 oxidoreductase activity, acting on a sulfur group of donors(GO:0016667)
0.0 0.2 GO:0016841 ammonia-lyase activity(GO:0016841)
0.0 0.1 GO:0050136 NADH dehydrogenase (ubiquinone) activity(GO:0008137) ubiquinone binding(GO:0048039) NADH dehydrogenase (quinone) activity(GO:0050136)
0.0 0.2 GO:0001140 transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding(GO:0001140)
0.0 0.4 GO:0005506 iron ion binding(GO:0005506)