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GSE80451: E.coli grown aerobically and anaerobically

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Results for Sigma38

Z-value: 5.30

Transcription factors associated with Sigma38

Gene Symbol Gene ID Gene Info
rpoS
rpoS RNA polymerase sigma factor RpoS

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
rpoS-0.922.6e-02Click!

Activity profile of Sigma38 motif

Sorted Z-values of Sigma38 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
astCADBE 14.68
astA
astB
astC
astD
astE
arginine succinyltransferase
succinylarginine dihydrolase
succinylornithine transaminase
aldehyde dehydrogenase
succinylglutamate desuccinylase
osmB 14.17
osmB
OsmB osmotically inducible lipoprotein
cfa 11.58
cfa
cyclopropane fatty acyl phospholipid synthase
bolA 11.36
bolA
BolA DNA-binding transcriptional dual regulator
glgS 9.97
glgS
surface composition regulator
pfkB 9.69
pfkB
6-phosphofructokinase II
ytfK 9.56
ytfK
conserved protein
blc 9.09
blc
outer membrane lipoprotein (lipocalin)
ihfA 8.84
ihfA
integration host factor (IHF), α subunit
uspB 8.12
uspB
predicted universal stress (ethanol tolerance) protein B
adhE 8.01
adhE
aldehyde-alcohol dehydrogenase
pykF 7.89
pykF
pyruvate kinase I
wrbA-yccJ 7.30
wrbA
yccJ
NAD(P)H:quinone oxidoreductase
predicted protein
yciG 7.13
yciG
predicted protein
crr 7.00
crr
Enzyme IIAGlc; Crr
ybiI 6.95
ybiI
conserved protein
sodC 6.92
sodC
superoxide dismutase (Cu-Zn)
ybjP 6.79
ybjP
predicted lipoprotein
csrA 6.77
csrA
carbon storage regulator; pleiotropic regulatory protein for carbon source metabolism
gadBC 6.26
gadB
gadC
glutamate decarboxylase B subunit
glutamic acid:4-aminobutyrate antiporter
talA-tktB 6.20
talA
tktB
transaldolase A
transketolase II
ryjA 6.02
ryjA
RyjA
bsmA 5.80
bsmA
conserved protein
osmC 5.58
osmC
osmotically inducible peroxiredoxin
yhfG-fic-pabA 5.56
fic
pabA
yhfG
stationary-phase protein
aminodeoxychorismate synthase component 2
predicted protein
tam 5.55
tam
trans-aconitate 2-methyltransferase
rssB 5.18
rssB
regulator of RpoS
patA 5.04
patA
putrescine aminotransferase
yggE 4.93
yggE
conserved protein
ydcSTUV-patD 4.85
patD
ydcV
ydcT
ydcU
ydcS
γ-aminobutyraldehyde dehydrogenase
putative transport protein, ABC family - membrane component
putative transport protein, ABC superfamily - ATP binding component
putative transport protein, ABC superfamily - membrane component
putative transport protein, ABC superfamily - periplasmic binding protein / polyhydroxybutyrate synthase
msyB 4.74
msyB
acidic protein that suppresses heat sensitivity of a secY mutant
ldcC 4.69
ldcC
lysine decarboxylase 2
tktB 4.69
tktB
transketolase II
dkgA 4.65
dkgA
methylglyoxal reductase/isobutyraldehyde reductase/β-keto ester reductase/2,5-diketo-D-gluconate reductase
fumC 4.63
fumC
fumarase C
yciGFE 4.62
yciG
yciF
yciE
predicted protein
conserved protein
conserved protein
treF 4.51
treF
cytoplasmic trehalase
kbp 4.33
kbp
K+ binding protein
luxS 4.33
luxS
S-ribosylhomocysteine lyase
ssrS 4.29
ssrS
6S RNA
iraD 4.19
iraD
inhibitor of σS proteolysis
acnA 4.17
acnA
aconitate hydratase 1
ssrS-fau 3.96
ssrS
fau
6S RNA
5-formyltetrahydrofolate cyclo-ligase
lsrACDBFG-tam 3.92
lsrA
lsrC
lsrB
lsrD
lsrG
lsrF
tam
AI-2 ABC transporter - ATP binding subunit
Autoinducer-2 ABC transporter - membrane subunit
autoinducer-2 ABC transporter - periplasmic binding protein
Autoinducer-2 ABC transporter - membrane subunit
phospho-AI-2 isomerase
3-hydroxy-2,4-pentadione 5-phosphate thiolase
trans-aconitate 2-methyltransferase
fadL 3.88
fadL
long-chain fatty acid outer membrane porin; bacteriophage T2 receptor
aldB 3.87
aldB
acetaldehyde dehydrogenase
proP 3.76
proP
osmolyte:H+ symporter ProP
yiaG 3.72
yiaG
predicted transcriptional regulator
yabI 3.46
yabI
conserved inner membrane protein
ada-alkB 3.26
alkB
ada
AlkB repair system for alkylated DNA and RNA
Ada DNA-binding transcriptional dual regulator / DNA repair protein
yhjG 3.15
yhjG
predicted outer membrane biogenesis protein
treA 3.10
treA
periplasmic trehalase
fbaB 3.07
fbaB
fructose bisphosphate aldolase class I
ydbK-ompN 3.06
ydbK
ompN
pyruvate:flavodoxin oxidoreductase
outer membrane pore protein N, non-specific
yhiM 2.96
yhiM
inner membrane protein with a role in acid resistance
katE 2.82
katE
catalase II
pdeR 2.69
pdeR
cyclic di-GMP phosphodiesterase
cbpAM 2.69
cbpM
cbpA
chaperone modulator protein CbpM
chaperone with DnaK; curved DNA-binding protein
pdeC 2.42
pdeC
predicted c-di-GMP-specific phosphodiesterase
poxB 2.15
poxB
pyruvate oxidase
gadE 2.04
gadE
GadE DNA-binding transcriptional activator
rssAB 1.99
rssA
rssB
conserved protein
regulator of RpoS
speB 1.96
speB
agmatinase
osmF-yehYXW 1.79
osmF
yehW
yehX
yehY
glycine betaine ABC transporter - periplasmic binding protein
glycine betaine ABC transporter - putative membrane subunit
glycine betaine ABC transporter - putative ATP binding subunit
glycine betaine ABC transporter - putative membrane subunit
araFGH 1.55
araF
araG
araH
arabinose ABC transporter - periplasmic binding protein
arabinose ABC transporter - ATP binding subunit
arabinose ABC transporter - membrane subunit
dhaKLM 1.48
dhaK
dhaM
dhaL
dihydroxyacetone kinase subunit K
dihydroxyacetone kinase subunit M and protein-acetyllysine deacetylase
dihydroxyacetone kinase subunit L
ecnB 0.82
ecnB
bacteriolytic entericidin B lipoprotein
otsA 0.81
otsA
trehalose-6-phosphate synthase
nhaAR 0.75
nhaA
nhaR
Na+:H+ antiporter NhaA
NhaR transcriptional activator
narU 0.66
narU
nitrate / nitrite transporter NarU
evgAS 0.58
evgA
evgS
EvgA transcriptional activator
EvgS sensory histidine kinase
alkA 0.56
alkA
3-methyl-adenine DNA glycosylase II, inducible
yeiL 0.56
yeiL
YeiL DNA-binding transcriptional activator
gadAX 0.49
gadX
gadA
GadX DNA-binding transcriptional dual regulator
glutamate decarboxylase A subunit
ydhYVWXUT 0.49
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
dhaR 0.42
dhaR
DhaR DNA-binding transcriptional dual regulator
hdeAB-yhiD 0.16
yhiD
hdeB
hdeA
inner membrane protein YhiD
HdeB monomer
HdeA monomer, chaperone active form
gadXW 0.05
gadW
gadX
GadW DNA-binding transcriptional dual regulator
GadX DNA-binding transcriptional dual regulator

Network of associatons between targets according to the STRING database.

First level regulatory network of Sigma38

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
8.0 8.0 GO:0006067 ethanol metabolic process(GO:0006067)
5.0 10.0 GO:1900231 regulation of single-species biofilm formation on inanimate substrate(GO:1900231) negative regulation of single-species biofilm formation on inanimate substrate(GO:1900232)
4.9 14.7 GO:0006527 succinate metabolic process(GO:0006105) arginine catabolic process(GO:0006527)
4.6 13.8 GO:0045912 negative regulation of carbohydrate metabolic process(GO:0045912)
4.0 12.0 GO:0097305 response to alcohol(GO:0097305)
3.1 9.4 GO:0071474 cellular hyperosmotic response(GO:0071474)
2.4 11.8 GO:0071978 bacterial-type flagellum-dependent swarming motility(GO:0071978)
2.3 6.9 GO:0006801 superoxide metabolic process(GO:0006801)
2.3 6.8 GO:0051454 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)
2.0 12.2 GO:0006972 hyperosmotic response(GO:0006972)
1.8 10.9 GO:0009052 pentose-phosphate shunt, non-oxidative branch(GO:0009052)
1.6 3.3 GO:0044728 DNA methylation or demethylation(GO:0044728)
1.6 9.5 GO:0009396 folic acid-containing compound biosynthetic process(GO:0009396) pteridine-containing compound biosynthetic process(GO:0042559)
1.5 4.6 GO:0006108 malate metabolic process(GO:0006108)
1.4 4.3 GO:0046498 S-adenosylmethionine cycle(GO:0033353) S-adenosylhomocysteine metabolic process(GO:0046498) S-adenosylmethionine metabolic process(GO:0046500)
1.4 4.2 GO:0009895 negative regulation of catabolic process(GO:0009895) regulation of protein catabolic process(GO:0042176) negative regulation of protein catabolic process(GO:0042177)
1.4 4.2 GO:0006097 glyoxylate cycle(GO:0006097)
1.2 7.2 GO:0030162 regulation of proteolysis(GO:0030162)
1.1 17.6 GO:0006096 glycolytic process(GO:0006096)
1.1 3.2 GO:0070201 regulation of protein localization(GO:0032880) regulation of protein transport(GO:0051223) regulation of establishment of protein localization(GO:0070201)
1.0 5.0 GO:0042542 response to hydrogen peroxide(GO:0042542)
0.8 11.6 GO:0030258 lipid modification(GO:0030258)
0.8 4.9 GO:0015931 nucleobase-containing compound transport(GO:0015931)
0.7 0.7 GO:0030641 regulation of pH(GO:0006885) cellular monovalent inorganic cation homeostasis(GO:0030004) regulation of cellular pH(GO:0030641) regulation of intracellular pH(GO:0051453) monovalent inorganic cation homeostasis(GO:0055067)
0.7 4.9 GO:0034614 cellular response to reactive oxygen species(GO:0034614)
0.6 3.0 GO:0071229 cellular response to acid chemical(GO:0071229)
0.6 4.7 GO:0009068 aspartate family amino acid catabolic process(GO:0009068)
0.5 1.5 GO:0042882 L-arabinose transport(GO:0042882)
0.5 1.5 GO:0006071 glycerol metabolic process(GO:0006071)
0.3 3.8 GO:0006869 lipid transport(GO:0006869)
0.3 6.8 GO:0051262 protein tetramerization(GO:0051262) protein homotetramerization(GO:0051289)
0.3 0.6 GO:0035510 DNA modification(GO:0006304) DNA dealkylation involved in DNA repair(GO:0006307) DNA dealkylation(GO:0035510)
0.3 3.1 GO:0034219 carbohydrate transmembrane transport(GO:0034219)
0.2 0.7 GO:0015707 nitrite transport(GO:0015707)
0.2 1.4 GO:0009438 methylglyoxal metabolic process(GO:0009438) methylglyoxal catabolic process(GO:0051596)
0.1 1.7 GO:0043086 negative regulation of catalytic activity(GO:0043086)
0.1 2.0 GO:0010212 response to ionizing radiation(GO:0010212)
0.1 0.7 GO:0010447 response to acidic pH(GO:0010447)
0.0 0.5 GO:0010038 response to metal ion(GO:0010038)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.9 5.6 GO:0005950 anthranilate synthase complex(GO:0005950)
0.6 7.0 GO:0031234 extrinsic component of cytoplasmic side of plasma membrane(GO:0031234)
0.4 4.9 GO:0071575 integral component of external side of plasma membrane(GO:0071575)
0.3 0.8 GO:0031225 anchored component of membrane(GO:0031225)
0.2 80.2 GO:0005829 cytosol(GO:0005829)
0.0 1.7 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
4.2 16.6 GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines(GO:0016813)
3.2 9.7 GO:0008443 phosphofructokinase activity(GO:0008443)
2.5 7.6 GO:0015927 trehalase activity(GO:0015927)
2.3 6.9 GO:0004784 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
1.9 5.6 GO:0051920 peroxiredoxin activity(GO:0051920)
1.9 5.6 GO:0015199 amino-acid betaine transmembrane transporter activity(GO:0015199) quaternary ammonium group transmembrane transporter activity(GO:0015651)
1.7 8.7 GO:0004029 aldehyde dehydrogenase (NAD) activity(GO:0004029)
1.6 10.9 GO:0016744 transferase activity, transferring aldehyde or ketonic groups(GO:0016744)
1.5 7.3 GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor(GO:0016655)
1.4 6.8 GO:0048027 mRNA 5'-UTR binding(GO:0048027)
1.3 3.9 GO:0022836 gated channel activity(GO:0022836) transmembrane receptor activity(GO:0099600)
1.3 3.8 GO:0004033 aldo-keto reductase (NADP) activity(GO:0004033)
1.1 3.3 GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors(GO:0016706)
1.0 4.2 GO:0043856 anti-sigma factor antagonist activity(GO:0043856)
1.0 3.1 GO:0004332 fructose-bisphosphate aldolase activity(GO:0004332)
1.0 5.1 GO:0071111 cyclic-guanylate-specific phosphodiesterase activity(GO:0071111)
1.0 4.0 GO:0016882 cyclo-ligase activity(GO:0016882)
0.9 2.8 GO:0004096 catalase activity(GO:0004096)
0.9 4.6 GO:0004333 fumarate hydratase activity(GO:0004333)
0.7 0.7 GO:0015491 cation:cation antiporter activity(GO:0015491)
0.7 16.9 GO:0008757 S-adenosylmethionine-dependent methyltransferase activity(GO:0008757)
0.7 5.8 GO:0000989 transcription factor activity, transcription factor binding(GO:0000989) sigma factor antagonist activity(GO:0016989)
0.5 4.3 GO:0030955 potassium ion binding(GO:0030955)
0.5 1.5 GO:0015147 L-arabinose transmembrane transporter activity(GO:0015147) carbohydrate-transporting ATPase activity(GO:0043211)
0.5 8.7 GO:0016831 carboxy-lyase activity(GO:0016831)
0.4 4.3 GO:0016846 carbon-sulfur lyase activity(GO:0016846)
0.4 4.2 GO:0044822 mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.4 2.7 GO:0043566 bent DNA binding(GO:0003681) structure-specific DNA binding(GO:0043566)
0.3 5.2 GO:0016301 kinase activity(GO:0016301)
0.3 0.7 GO:0015113 nitrite transmembrane transporter activity(GO:0015113)
0.3 8.0 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor(GO:0016616)
0.2 0.6 GO:0019104 DNA N-glycosylase activity(GO:0019104)
0.2 1.5 GO:0019213 deacetylase activity(GO:0019213)
0.1 6.3 GO:0016773 phosphotransferase activity, alcohol group as acceptor(GO:0016773)
0.1 0.8 GO:0008483 transaminase activity(GO:0008483)
0.1 0.2 GO:0051087 chaperone binding(GO:0051087)
0.0 0.7 GO:0050660 flavin adenine dinucleotide binding(GO:0050660)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
1.1 3.3 PID P73PATHWAY p73 transcription factor network

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
1.3 4.0 REACTOME NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX Genes involved in Nonsense Mediated Decay Enhanced by the Exon Junction Complex
1.1 3.3 REACTOME PURINE SALVAGE Genes involved in Purine salvage