Project

GSE80451: E.coli grown aerobically and anaerobically

Navigation
Downloads

Results for Sigma54

Z-value: 1.02

Transcription factors associated with Sigma54

Gene Symbol Gene ID Gene Info
rpoN
rpoN RNA polymerase sigma factor RpoN

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
rpoN-0.968.9e-03Click!

Activity profile of Sigma54 motif

Sorted Z-values of Sigma54 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
zraP 4.25
zraP
zinc responsive, periplasmic protein with chaperone activity
glnA 2.08
glnA
glutamine synthetase
relA 1.77
relA
GDP pyrophosphokinase/GTP pyrophosphokinase
emrD 1.76
emrD
multidrug efflux pump EmrD
htpG 1.43
htpG
molecular chaperone, HSP90 family
puuP 1.20
puuP
putrescine:H+ symporter PuuP
flhDC 1.13
flhC
flhD
FlhC transcriptional dual regulator
FlhD transcriptional dual regulator
atoDAEB 0.98
atoB
atoA
atoD
atoE
acetyl-CoA acetyltransferase
acetyl-CoA:acetoacetyl-CoA transferase, β subunit
acetyl-CoA:acetoacetyl-CoA transferase, α subunit
predicted short chain fatty acid transporter
acrD 0.96
acrD
AcrAD-TolC multidrug efflux pump - permease subunit
ddpXABCDF 0.81
ddpX
ddpD
ddpF
ddpA
ddpB
ddpC
D-Ala-D-Ala dipeptidase
YddP
YddO
YddS
YddR
YddQ
norVW 0.68
norW
norV
NADH:flavorubredoxin reductase
flavorubredoxin
radD 0.61
radD
predicted ATP-dependent helicase; implicated in DNA repair
xdhABC 0.55
xdhA
xdhB
xdhC
xanthine dehydrogenase subunit
xanthine dehydrogenase subunit, FAD-binding domain
xanthine dehydrogenase, Fe-S subunit
glnALG 0.49
glnL
glnA
glnG
NtrB
glutamine synthetase
NtrC transcriptional dual regulator
crl 0.45
crl
RNA polymerase holoenzyme assembly factor Crl
zraSR 0.43
zraS
zraR
ZraS sensory histidine kinase
ZraR transcriptional activator
yhjC 0.41
yhjC
predicted DNA-binding transcriptional regulator
nikABCDER 0.40
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
dcuD 0.30
dcuD
putative transport protein, C4-dicarboxylate uptake C family
potFGHI 0.29
potI
potH
potG
potF
putrescine ABC transporter - membrane subunit
putrescine ABC transporter - membrane subunit
putrescine ABC transporter - ATP binding subunit
putrescine ABC transporter - periplasmic binding protein
hyfABCDEFGHIJR-focB 0.28
hyfJ
hyfI
hyfH
hyfC
hyfB
hyfA
hyfG
hyfF
hyfE
hyfD
hyfR
focB
hydrogenase 4 component J, putative protein processing element
hydrogenase 4, small subunit
hydrogenase 4, component H
hydrogenase 4, component C
hydrogenase 4, component B
hydrogenase 4, component A
hydrogenase 4, large subunit
hydrogenase 4, component F
hydrogenase 4, component E
hydrogenase 4, component D
HyfR DNA-binding transcriptional activator
FocB formate FNT transporter
pspABCDE 0.22
pspE
pspD
pspC
pspB
pspA
thiosulfate sulfurtransferase
peripheral inner membrane phage-shock protein
PspC transcriptional regulator; toxin of a PspC-PspB toxin-antitoxin pair
stimulates PspC-mediated transcriptional activation of the psp operon; antitoxin of a PspC-PspB toxin-antitoxin pair
regulatory protein for the phage shock operon, protects membrane integrity
rpoH 0.20
rpoH
RNA polymerase, sigma 32 (sigma H) factor
fdhF 0.20
fdhF
formate dehydrogenase H
yaaU 0.19
yaaU
putative transport protein YaaU, major facilitator superfamily (MFS)
aslB 0.18
aslB
predicted anaerobic sulfatase maturation enzyme
nac 0.14
nac
Nac DNA-binding transcriptional dual regulator
yahE 0.12
yahE
predicted protein
glnK-amtB 0.06
glnK
amtB
nitrogen regulatory protein GlnK
ammonia / ammonium transporter
hydN-hypF 0.04
hypF
hydN
hydrogenase maturation protein, carbamoyltransferase
putative electron transport protein HydN

Network of associatons between targets according to the STRING database.

First level regulatory network of Sigma54

PNG image of the network

In order to view interactive SVG image please either update your browser to latest version or install SVG plugin.
View svg image
View png image

Gene Ontology Analysis

Gene overrepresentation in biological process category:

Log-likelihood per target  Total log-likelihood Term Description
0.9 2.6 GO:0019676 ammonia assimilation cycle(GO:0019676)
0.6 1.8 GO:0015969 guanosine tetraphosphate metabolic process(GO:0015969) purine ribonucleoside bisphosphate metabolic process(GO:0034035)
0.5 1.5 GO:0015846 polyamine transport(GO:0015846) putrescine transport(GO:0015847)
0.2 0.7 GO:0046210 nitric oxide metabolic process(GO:0046209) nitric oxide catabolic process(GO:0046210) cellular response to nitrogen compound(GO:1901699) cellular response to reactive nitrogen species(GO:1902170)
0.2 0.6 GO:0010501 RNA secondary structure unwinding(GO:0010501)
0.2 0.5 GO:0046100 purine nucleobase catabolic process(GO:0006145) hypoxanthine metabolic process(GO:0046100)
0.1 1.0 GO:0006855 drug transmembrane transport(GO:0006855)
0.1 1.0 GO:0006635 fatty acid beta-oxidation(GO:0006635)
0.1 0.8 GO:0006024 aminoglycan biosynthetic process(GO:0006023) glycosaminoglycan biosynthetic process(GO:0006024) peptidoglycan biosynthetic process(GO:0009252)
0.1 0.2 GO:0001121 transcription from bacterial-type RNA polymerase promoter(GO:0001121)
0.1 0.4 GO:0006935 chemotaxis(GO:0006935) taxis(GO:0042330)
0.1 1.4 GO:0006457 protein folding(GO:0006457)
0.1 0.2 GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity(GO:0043433)
0.0 0.2 GO:0015942 formate metabolic process(GO:0015942)
0.0 0.3 GO:0010043 response to zinc ion(GO:0010043)
0.0 0.5 GO:0043623 cellular protein complex assembly(GO:0043623)
0.0 0.1 GO:0006808 regulation of nitrogen utilization(GO:0006808)
0.0 0.1 GO:2000142 regulation of DNA-templated transcription, initiation(GO:2000142)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 1.8 GO:0005618 cell wall(GO:0005618)
0.0 4.6 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)
0.0 6.2 GO:0016020 membrane(GO:0016020)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.4 4.3 GO:0050897 cobalt ion binding(GO:0050897)
0.6 2.6 GO:0016211 ammonia ligase activity(GO:0016211)
0.6 1.8 GO:0008893 GTP diphosphokinase activity(GO:0008728) guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity(GO:0008893) diphosphoric monoester hydrolase activity(GO:0016794)
0.3 1.0 GO:0008410 CoA-transferase activity(GO:0008410)
0.3 1.0 GO:0015307 drug:proton antiporter activity(GO:0015307)
0.2 0.8 GO:0008235 metalloexopeptidase activity(GO:0008235)
0.2 0.6 GO:0008186 RNA helicase activity(GO:0003724) ATP-dependent RNA helicase activity(GO:0004004) RNA-dependent ATPase activity(GO:0008186)
0.2 1.2 GO:0015101 organic cation transmembrane transporter activity(GO:0015101)
0.1 0.5 GO:0016725 oxidoreductase activity, acting on CH or CH2 groups(GO:0016725)
0.1 0.4 GO:0015099 nickel cation transmembrane transporter activity(GO:0015099)
0.1 0.3 GO:0008137 NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
0.1 0.4 GO:0000156 phosphorelay response regulator activity(GO:0000156)
0.1 0.2 GO:0030151 molybdenum ion binding(GO:0030151)
0.1 0.2 GO:0005543 phospholipid binding(GO:0005543)
0.0 0.7 GO:0016661 oxidoreductase activity, acting on other nitrogenous compounds as donors(GO:0016661)
0.0 0.2 GO:0000990 transcription factor activity, core RNA polymerase binding(GO:0000990) core DNA-dependent RNA polymerase binding promoter specificity activity(GO:0000996) sigma factor activity(GO:0016987)
0.0 1.4 GO:0042623 ATPase activity, coupled(GO:0042623)
0.0 0.1 GO:0008519 ammonium transmembrane transporter activity(GO:0008519)
0.0 0.0 GO:0016743 carboxyl- or carbamoyltransferase activity(GO:0016743)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.6 1.8 PID ANGIOPOIETIN RECEPTOR PATHWAY Angiopoietin receptor Tie2-mediated signaling

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.6 1.8 REACTOME DEVELOPMENTAL BIOLOGY Genes involved in Developmental Biology