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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for Sigma54

Z-value: 0.81

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-0.902.4e-03Click!

Activity profile of Sigma54 motif

Sorted Z-values of Sigma54 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
rtcR 4.00
rtcR
RtcR DNA-binding transcriptional activator
dcuD 3.49
dcuD
putative transport protein, C4-dicarboxylate uptake C family
nac 3.02
nac
Nac DNA-binding transcriptional dual regulator
ygfK-ssnA 2.79
ygfK
ssnA
predicted oxidoreductase, Fe-S subunit
predicted chlorohydrolase/aminohydrolase
glnK-amtB 2.68
glnK
amtB
nitrogen regulatory protein GlnK
ammonia / ammonium transporter
zraP 2.57
zraP
zinc responsive, periplasmic protein with chaperone activity
hyfABCDEFGHIJR-focB 2.22
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
hycABCDEFGHI 2.20
hycD
hycE
hycF
hycG
hycA
hycB
hycC
hycH
hycI
hydrogenase 3, membrane subunit
hydrogenase 3, large subunit
formate hydrogenlyase complex iron-sulfur protein
hydrogenase 3 and formate hydrogenlyase complex, HycG subunit
regulator of the transcriptional regulator FhlA
hydrogenase 3, Fe-S subunit
hydrogenase 3, membrane subunit
protein required for maturation of hydrogenase 3
hydrogenase 3 maturation protease
yhdWXYZ 2.05
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
rtcBA 1.62
rtcB
rtcA
RNA-splicing ligase RtcB
RNA 3'-terminal phosphate cyclase
atoDAEB 1.37
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 1.31
xdhA
xdhB
xdhC
xanthine dehydrogenase subunit
xanthine dehydrogenase subunit, FAD-binding domain
xanthine dehydrogenase, Fe-S subunit
chaC 1.26
chaC
predicted glutathione-specific gamma-glutamylcyclotransferase
potFGHI 1.01
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
yahE 0.98
yahE
predicted protein
pspG 0.96
pspG
phage shock protein G
yhjC 0.89
yhjC
predicted DNA-binding transcriptional regulator
acrD 0.87
acrD
AcrAD-TolC multidrug efflux pump - permease subunit
aslB 0.86
aslB
predicted anaerobic sulfatase maturation enzyme
radD 0.80
radD
predicted ATP-dependent helicase; implicated in DNA repair
argT-hisJQMP 0.79
hisM
hisP
argT
hisQ
hisJ
lysine/arginine/ornithine ABC transporter / histidine ABC transporter - membrane subunit
lysine / arginine / ornithine ABC transporter / histidine ABC transporter - ATP binding subunit
lysine / arginine / ornithine ABC transporter - periplasmic binding protein
lysine / arginine / ornithine ABC transporter / histidine ABC transporter - membrane subunit
histidine ABC transporter - periplasmic binding protein
actP 0.76
actP
acetate / glycolate : cation symporter
ddpXABCDF 0.71
ddpX
ddpD
ddpF
ddpA
ddpB
ddpC
D-Ala-D-Ala dipeptidase
YddP
YddO
YddS
YddR
YddQ
norVW 0.67
norW
norV
NADH:flavorubredoxin reductase
flavorubredoxin
puuP 0.59
puuP
putrescine:H+ symporter PuuP
crl 0.36
crl
RNA polymerase holoenzyme assembly factor Crl
hydN-hypF 0.34
hypF
hydN
hydrogenase maturation protein, carbamoyltransferase
putative electron transport protein HydN
rutABCDEFG 0.24
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
astCADBE 0.19
astA
astB
astC
astD
astE
arginine succinyltransferase
succinylarginine dihydrolase
succinylornithine transaminase
aldehyde dehydrogenase
succinylglutamate desuccinylase
glnALG 0.00
glnL
glnA
glnG
NtrB
glutamine synthetase
NtrC transcriptional dual regulator

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
0.9 2.7 GO:0006808 regulation of nitrogen utilization(GO:0006808)
0.5 1.6 GO:0015846 polyamine transport(GO:0015846) putrescine transport(GO:0015847)
0.5 3.4 GO:0015740 C4-dicarboxylate transport(GO:0015740)
0.4 2.2 GO:0016485 protein processing(GO:0016485)
0.4 1.3 GO:0046100 purine nucleobase catabolic process(GO:0006145) hypoxanthine metabolic process(GO:0046100)
0.4 1.6 GO:0042245 RNA repair(GO:0042245)
0.3 1.3 GO:0043171 peptide catabolic process(GO:0043171)
0.3 0.8 GO:0015710 tellurite transport(GO:0015710)
0.3 0.8 GO:0019626 short-chain fatty acid catabolic process(GO:0019626)
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 0.8 GO:0010501 RNA secondary structure unwinding(GO:0010501)
0.2 0.8 GO:1903401 L-arginine import(GO:0043091) L-amino acid import(GO:0043092) arginine import(GO:0090467) L-arginine import across plasma membrane(GO:0097638) L-arginine import into cell(GO:1902765) L-arginine transmembrane transport(GO:1903400) L-lysine transmembrane transport(GO:1903401) arginine transmembrane transport(GO:1903826)
0.1 2.2 GO:0015718 monocarboxylic acid transport(GO:0015718)
0.1 0.9 GO:0006855 drug transmembrane transport(GO:0006855)
0.1 0.2 GO:0006105 succinate metabolic process(GO:0006105)
0.1 5.5 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)
0.1 0.2 GO:0015855 pyrimidine nucleobase catabolic process(GO:0006208) nucleobase transport(GO:0015851) pyrimidine nucleobase transport(GO:0015855)
0.1 0.7 GO:0009252 aminoglycan biosynthetic process(GO:0006023) glycosaminoglycan biosynthetic process(GO:0006024) peptidoglycan biosynthetic process(GO:0009252)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 2.2 GO:1990204 oxidoreductase complex(GO:1990204)
0.0 10.5 GO:0005887 integral component of plasma membrane(GO:0005887)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.9 2.6 GO:0050897 cobalt ion binding(GO:0050897)
0.7 2.2 GO:0008137 NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
0.5 1.4 GO:0008410 CoA-transferase activity(GO:0008410)
0.4 3.3 GO:0008519 ammonium transmembrane transporter activity(GO:0008519)
0.3 1.3 GO:0016755 transferase activity, transferring amino-acyl groups(GO:0016755)
0.3 0.9 GO:0015307 drug:proton antiporter activity(GO:0015307)
0.3 0.8 GO:0015189 L-lysine transmembrane transporter activity(GO:0015189)
0.3 1.3 GO:0016725 oxidoreductase activity, acting on CH or CH2 groups(GO:0016725)
0.3 0.8 GO:0015118 tellurite transmembrane transporter activity(GO:0015118) tellurite uptake transmembrane transporter activity(GO:0015654)
0.2 0.8 GO:0008186 RNA helicase activity(GO:0003724) ATP-dependent RNA helicase activity(GO:0004004) RNA-dependent ATPase activity(GO:0008186)
0.2 0.2 GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines(GO:0016813)
0.2 0.7 GO:0008235 metalloexopeptidase activity(GO:0008235)
0.1 7.9 GO:0003700 transcription factor activity, sequence-specific DNA binding(GO:0003700)
0.1 2.2 GO:0004175 endopeptidase activity(GO:0004175)
0.1 0.3 GO:0016743 carboxyl- or carbamoyltransferase activity(GO:0016743)
0.1 0.2 GO:0005350 monooxygenase activity(GO:0004497) pyrimidine nucleobase transmembrane transporter activity(GO:0005350)
0.1 1.6 GO:0030145 manganese ion binding(GO:0030145)
0.1 0.7 GO:0016661 oxidoreductase activity, acting on other nitrogenous compounds as donors(GO:0016661)
0.0 2.8 GO:0016491 oxidoreductase activity(GO:0016491)