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

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Results for Sigma54

Z-value: 2.64

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-0.965.9e-15Click!

Activity profile of Sigma54 motif

Sorted Z-values of Sigma54 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
yeaGH 31.88
yeaG
yeaH
protein kinase
conserved protein
gltI-sroC-gltJKL 27.45
sroC
gltI
gltK
gltJ
gltL
SroC
glutamate / aspartate ABC transporter - periplasmic binding protein
glutamate / aspartate ABC transporter - membrane subunit
glutamate / aspartate ABC transporter - membrane subunit
glutamate / aspartate ABC transporter - ATP binding subunit
glmY 21.90
glmY
GlmY
astCADBE 21.35
astA
astB
astC
astD
astE
arginine succinyltransferase
succinylarginine dihydrolase
succinylornithine transaminase
aldehyde dehydrogenase
succinylglutamate desuccinylase
ibpB 19.83
ibpB
small heat shock protein IbpB
nac 19.76
nac
Nac DNA-binding transcriptional dual regulator
prpBCDE 19.42
prpD
prpE
prpB
prpC
2-methylcitrate dehydratase
propionyl-CoA synthetase
2-methylisocitrate lyase
2-methylcitrate synthase
zraP 19.26
zraP
zinc responsive, periplasmic protein with chaperone activity
rhaD 18.76
rhaD
rhamnulose-1-phosphate aldolase
yaaU 18.53
yaaU
putative transport protein YaaU, major facilitator superfamily (MFS)
emrD 17.51
emrD
multidrug efflux pump EmrD
pspG 17.43
pspG
phage shock protein G
hydN-hypF 17.08
hypF
hydN
hydrogenase maturation protein, carbamoyltransferase
putative electron transport protein HydN
dcuD 16.11
dcuD
putative transport protein, C4-dicarboxylate uptake C family
rtcR 16.02
rtcR
RtcR DNA-binding transcriptional activator
yahE 15.57
yahE
predicted protein
ygfK-ssnA 15.37
ygfK
ssnA
predicted oxidoreductase, Fe-S subunit
predicted chlorohydrolase/aminohydrolase
actP 12.54
actP
acetate / glycolate : cation symporter
atoDAEB 11.21
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
xdhABC 10.50
xdhA
xdhB
xdhC
xanthine dehydrogenase subunit
xanthine dehydrogenase subunit, FAD-binding domain
xanthine dehydrogenase, Fe-S subunit
rtcBA 9.63
rtcB
rtcA
RNA-splicing ligase RtcB
RNA 3'-terminal phosphate cyclase
rpoH 9.15
rpoH
RNA polymerase, sigma 32 (sigma H) factor
rutABCDEFG 9.05
rutC
rutB
rutA
rutG
rutF
rutE
rutD
predicted aminoacrylate peracid reductase
peroxyureidoacrylate / ureidoacrylate amido hydrolase
pyrimidine oxygenase
uracil:H+ symporter RutG
flavin reductase
predicted malonic semialdehyde reductase
predicted aminoacrylate hydrolase
aslB 8.32
aslB
predicted anaerobic sulfatase maturation enzyme
hyfABCDEFGHIJR-focB 6.62
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
nikABCDER 4.82
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
pspABCDE 4.70
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
norVW 4.17
norW
norV
NADH:flavorubredoxin reductase
flavorubredoxin
yhjC 4.03
yhjC
predicted DNA-binding transcriptional regulator
yhdWXYZ 3.37
yhdZ
yhdY
yhdX
yhdW
putative transport protein, ABC superfamily - periplasmic binding protein
putative transport protein, ABC superfamily - membrane component
putative transport protein, ABC superfamily - ATP-binding component
putative transport protein, ABC superfamily - membrane component
hypABCDE-fhlA 2.71
fhlA
hypE
hypD
hypA
hypC
hypB
FhlA transcriptional activator
hydrogenase maturation protein, carbamoyl dehydratase
HypD, scaffold protein for assembly of the Fe-(CN)2CO cofactor
accessory protein for nickel incorporation into hydrogenase 3
HypC, protein involved in hydrogenase 3 maturation
accessory protein for nickel incorporation into hydrogenase isoenzymes
zraSR 2.45
zraS
zraR
ZraS sensory histidine kinase
ZraR transcriptional activator
hypABCDE 2.00
hypE
hypD
hypA
hypC
hypB
hydrogenase maturation protein, carbamoyl dehydratase
HypD, scaffold protein for assembly of the Fe-(CN)2CO cofactor
accessory protein for nickel incorporation into hydrogenase 3
HypC, protein involved in hydrogenase 3 maturation
accessory protein for nickel incorporation into hydrogenase isoenzymes
ddpXABCDF 1.72
ddpX
ddpD
ddpF
ddpA
ddpB
ddpC
D-Ala-D-Ala dipeptidase
YddP
YddO
YddS
YddR
YddQ
acrD 1.52
acrD
AcrAD-TolC multidrug efflux pump - permease subunit
relA 1.23
relA
GDP pyrophosphokinase/GTP pyrophosphokinase
chaC 1.04
chaC
predicted glutathione-specific gamma-glutamylcyclotransferase

Network of associatons between targets according to the STRING database.

First level regulatory network of Sigma54

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
10.2 30.6 GO:0019626 short-chain fatty acid catabolic process(GO:0019626)
7.3 43.6 GO:0015740 dicarboxylic acid transport(GO:0006835) C4-dicarboxylate transport(GO:0015740)
7.1 21.3 GO:0006527 succinate metabolic process(GO:0006105) arginine catabolic process(GO:0006527)
5.5 22.1 GO:0051707 response to biotic stimulus(GO:0009607) response to virus(GO:0009615) response to external biotic stimulus(GO:0043207) response to other organism(GO:0051707)
4.7 18.8 GO:0019301 rhamnose metabolic process(GO:0019299) rhamnose catabolic process(GO:0019301)
4.2 12.5 GO:0015710 tellurite transport(GO:0015710)
4.0 19.8 GO:1990169 stress response to copper ion(GO:1990169)
3.5 10.5 GO:0046100 purine nucleobase catabolic process(GO:0006145) hypoxanthine metabolic process(GO:0046100)
3.0 9.0 GO:0046113 nucleobase catabolic process(GO:0046113)
2.4 9.6 GO:0042245 RNA repair(GO:0042245)
2.3 9.2 GO:0001121 transcription from bacterial-type RNA polymerase promoter(GO:0001121)
1.4 4.2 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)
1.2 4.7 GO:0046892 protein dehydration(GO:0018249) peptidyl-S-carbamoyl-L-cysteine dehydration(GO:0046892)
1.1 20.5 GO:0051604 protein maturation(GO:0051604)
0.8 17.3 GO:0009267 cellular response to starvation(GO:0009267)
0.6 2.5 GO:0010043 response to zinc ion(GO:0010043)
0.6 4.8 GO:0098662 inorganic cation transmembrane transport(GO:0098662)
0.6 6.6 GO:2000142 regulation of DNA-templated transcription, initiation(GO:2000142)
0.5 1.0 GO:0044273 sulfur compound catabolic process(GO:0044273)
0.5 25.7 GO:1902680 positive regulation of transcription, DNA-templated(GO:0045893) positive regulation of RNA metabolic process(GO:0051254) positive regulation of RNA biosynthetic process(GO:1902680) positive regulation of nucleic acid-templated transcription(GO:1903508)
0.4 3.0 GO:0042594 response to starvation(GO:0042594)
0.4 18.5 GO:0006979 response to oxidative stress(GO:0006979)
0.2 1.5 GO:0006855 drug transmembrane transport(GO:0006855)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.8 9.4 GO:0031234 extrinsic component of cytoplasmic side of plasma membrane(GO:0031234)
0.4 19.3 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)
0.4 4.8 GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing(GO:0055052)
0.3 99.9 GO:0005886 plasma membrane(GO:0005886)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
6.4 19.3 GO:0050897 cobalt ion binding(GO:0050897)
5.7 17.1 GO:0016743 carboxyl- or carbamoyltransferase activity(GO:0016743)
5.3 21.3 GO:0016813 N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity(GO:0003992) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines(GO:0016813)
4.9 19.4 GO:0046912 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer(GO:0046912)
4.2 12.5 GO:0015654 tellurite transmembrane transporter activity(GO:0015118) tellurite uptake transmembrane transporter activity(GO:0015654) glycolate transmembrane transporter activity(GO:0043879)
3.7 11.2 GO:0003988 acetyl-CoA C-acyltransferase activity(GO:0003988) CoA-transferase activity(GO:0008410)
3.0 9.0 GO:0005350 monooxygenase activity(GO:0004497) pyrimidine nucleobase transmembrane transporter activity(GO:0005350)
2.2 6.6 GO:0008137 NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
2.1 10.5 GO:0016725 oxidoreductase activity, acting on CH or CH2 groups(GO:0016725)
1.8 9.2 GO:0016987 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)
1.6 4.8 GO:0015099 nickel cation transmembrane transporter activity(GO:0015099)
1.2 4.7 GO:0070025 carbon monoxide binding(GO:0070025)
1.2 4.7 GO:0005543 phospholipid binding(GO:0005543)
1.0 18.8 GO:0016832 aldehyde-lyase activity(GO:0016832)
0.9 12.9 GO:0016597 amino acid binding(GO:0016597)
0.8 1.5 GO:0015299 solute:proton antiporter activity(GO:0015299) drug:proton antiporter activity(GO:0015307)
0.7 17.2 GO:0004672 protein kinase activity(GO:0004672)
0.7 19.5 GO:0005506 iron ion binding(GO:0005506)
0.6 39.8 GO:0003700 transcription factor activity, sequence-specific DNA binding(GO:0003700)
0.6 1.7 GO:0008235 metalloexopeptidase activity(GO:0008235)
0.6 9.6 GO:0030145 manganese ion binding(GO:0030145)
0.4 1.2 GO:0016794 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:0016755 transferase activity, transferring amino-acyl groups(GO:0016755)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 1.2 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
0.4 1.2 REACTOME DEVELOPMENTAL BIOLOGY Genes involved in Developmental Biology