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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for Sigma38

Z-value: 0.91

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-0.275.2e-01Click!

Activity profile of Sigma38 motif

Sorted Z-values of Sigma38 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
talA-tktB 1.95
talA
tktB
transaldolase A
transketolase II
otsBA 1.01
otsA
otsB
trehalose-6-phosphate synthase
trehalose-6-phosphate phosphatase
tktB 0.97
tktB
transketolase II
ycgZ-ymgA-ariR-ymgC 0.93
ariR
ymgC
ymgA
ycgZ
regulator of acid resistance, influenced by indole
protein involved in biofilm formation
protein involved in biofilm formation
predicted protein
ybiI 0.93
ybiI
conserved protein
gadBC 0.92
gadB
gadC
glutamate decarboxylase B subunit
glutamic acid:4-aminobutyrate antiporter
yhjG 0.88
yhjG
predicted outer membrane biogenesis protein
osmF-yehYXW 0.87
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
ybgA-phr 0.74
ybgA
phr
conserved protein
deoxyribodipyrimidine photolyase (photoreactivation)
yciGFE 0.72
yciG
yciF
yciE
predicted protein
conserved protein
conserved protein
puuCBE 0.70
puuB
puuC
puuE
γ-glutamylputrescine oxidase
γ-glutamyl-γ-aminobutyraldehyde dehydrogenase
4-aminobutyrate aminotransferase
poxB 0.68
poxB
pyruvate oxidase
puuAP 0.66
puuP
puuA
putrescine:H+ symporter PuuP
glutamate-putrescine ligase
yiaG 0.64
yiaG
predicted transcriptional regulator
proP 0.63
proP
osmolyte:H+ symporter ProP
yjiY 0.61
yjiY
inner membrane protein - predicted transporter
otsA 0.60
otsA
trehalose-6-phosphate synthase
gabDTP 0.60
gabD
gabT
gabP
succinate-semialdehyde dehydrogenase (NADP+)
4-aminobutyrate aminotransferase
4-aminobutyrate:H+ symporter
acnA 0.55
acnA
aconitate hydratase 1
gadAX 0.53
gadX
gadA
GadX DNA-binding transcriptional dual regulator
glutamate decarboxylase A subunit
ecnB 0.53
ecnB
bacteriolytic entericidin B lipoprotein
kbp 0.52
kbp
K+ binding protein
yciG 0.51
yciG
predicted protein
cbpAM 0.48
cbpM
cbpA
chaperone modulator protein CbpM
chaperone with DnaK; curved DNA-binding protein
hchA 0.47
hchA
amino acid deglycase Hsp31
csgDEFG 0.47
csgG
csgF
csgE
csgD
curli secretion channel
curli assembly component
curli transport specificity factor
CsgD DNA-binding transcriptional dual regulator
tam 0.44
tam
trans-aconitate 2-methyltransferase
hofMNOP 0.43
hofM
hofO
hofN
hofP
protein involved in utilization of DNA as a carbon source
protein involved in utilization of DNA as a carbon source
protein involved in utilization of DNA as a carbon source
protein involved in utilization of DNA as a carbon source
csiD-lhgO-gabDTP 0.43
gabD
lhgO
gabP
csiD
gabT
succinate-semialdehyde dehydrogenase (NADP+)
L-2-hydroxyglutarate oxidase
4-aminobutyrate:H+ symporter
predicted protein
4-aminobutyrate aminotransferase
sdsN 0.42
sdsN
YecC3'
yffOP 0.42
yffO
yffP
CPZ-55 prophage; predicted protein
CPZ-55 prophage; predicted protein
ydbK-ompN 0.40
ydbK
ompN
pyruvate:flavodoxin oxidoreductase
outer membrane pore protein N, non-specific
lsrACDBFG-tam 0.40
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
gadE 0.39
gadE
GadE DNA-binding transcriptional activator
yeiL 0.38
yeiL
YeiL DNA-binding transcriptional activator
dkgB 0.38
dkgB
methylglyoxal reductase/4-nitrobenzaldehyde reductase/2,5-diketo-D-gluconate reductase
msyB 0.38
msyB
acidic protein that suppresses heat sensitivity of a secY mutant
blc 0.36
blc
outer membrane lipoprotein (lipocalin)
ydbD 0.33
ydbD
protein involved in detoxification of methylglyoxal
yhiM 0.31
yhiM
inner membrane protein with a role in acid resistance
katE 0.30
katE
catalase II
gpmM-envC-yibQ 0.28
envC
yibQ
gpmM
EnvC divisome associated factor, activator of peptidoglycan hydrolases
putative nucleoside (IDP) diphosphatase
2,3-bisphosphoglycerate-independent phosphoglycerate mutase
yihG 0.28
yihG
predicted endonuclease
yadV-htrE 0.27
htrE
yadV
putative outer membrane usher protein
probable pilin chaperone similar to PapD
ydcSTUV-patD 0.27
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
speC 0.25
speC
ornithine decarboxylase, biosynthetic
yhfG-fic-pabA 0.24
fic
pabA
yhfG
stationary-phase protein
aminodeoxychorismate synthase component 2
predicted protein
aldB 0.23
aldB
acetaldehyde dehydrogenase
puuDRCBE 0.22
puuR
puuC
puuB
puuD
puuE
PuuR DNA-binding transcriptional repressor
γ-glutamyl-γ-aminobutyraldehyde dehydrogenase
γ-glutamylputrescine oxidase
γ-glutamyl-γ-aminobutyrate hydrolase
4-aminobutyrate aminotransferase
dhaR 0.21
dhaR
DhaR DNA-binding transcriptional dual regulator
ryjA 0.19
ryjA
RyjA
treA 0.16
treA
periplasmic trehalase
osmB 0.15
osmB
OsmB osmotically inducible lipoprotein
narU 0.15
narU
nitrate / nitrite transporter NarU
treF 0.15
treF
cytoplasmic trehalase
rsd 0.14
rsd
regulator of σ70 (σD), stationary phase protein
asr 0.14
asr
acid shock protein
mpl 0.10
mpl
UDP-N-acetylmuramate:L-alanyl-γ-D-glutamyl-meso-diaminoheptanedioate-D-alanine ligase/UDP-N-acetylmuramate:L-alanyl-γ-D-glutamyl-meso-diaminopimelate ligase
dkgA 0.10
dkgA
methylglyoxal reductase/isobutyraldehyde reductase/β-keto ester reductase/2,5-diketo-D-gluconate reductase
ytfK 0.09
ytfK
conserved protein
iraD 0.09
iraD
inhibitor of σS proteolysis
hdfR 0.09
hdfR
HdfR DNA-binding transcriptional dual regulator
dgcC 0.08
dgcC
diguanylate cyclase
alkA 0.07
alkA
3-methyl-adenine DNA glycosylase II, inducible
rssB 0.07
rssB
regulator of RpoS
gadX 0.07
gadX
GadX DNA-binding transcriptional dual regulator
osmC 0.07
osmC
osmotically inducible peroxiredoxin
pykF 0.06
pykF
pyruvate kinase I
bolA 0.05
bolA
BolA DNA-binding transcriptional dual regulator
yddG 0.05
yddG
aromatic amino acid exporter
patA 0.03
patA
putrescine aminotransferase
sra 0.02
sra
30S ribosomal subunit protein S22
ydhYVWXUT 0.02
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
pcnB-folK 0.02
pcnB
folK
poly(A) polymerase I
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase

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
0.5 2.9 GO:0009052 pentose-phosphate shunt, non-oxidative branch(GO:0009052)
0.4 1.6 GO:0070417 cellular response to cold(GO:0070417)
0.4 1.2 GO:0071474 cellular hyperosmotic response(GO:0071474)
0.4 1.5 GO:0051454 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)
0.3 1.9 GO:0006598 polyamine catabolic process(GO:0006598) putrescine catabolic process(GO:0009447)
0.3 0.9 GO:0032880 regulation of protein localization(GO:0032880) regulation of protein transport(GO:0051223) regulation of establishment of protein localization(GO:0070201)
0.2 1.2 GO:0071978 bacterial-type flagellum-dependent swarming motility(GO:0071978)
0.2 0.6 GO:0006097 glyoxylate cycle(GO:0006097)
0.2 0.9 GO:0042450 ornithine metabolic process(GO:0006591) arginine biosynthetic process via ornithine(GO:0042450)
0.2 0.7 GO:0051595 response to methylglyoxal(GO:0051595) response to ketone(GO:1901654)
0.2 1.0 GO:0006972 hyperosmotic response(GO:0006972)
0.1 0.4 GO:0015976 carbon utilization(GO:0015976)
0.1 0.3 GO:0000920 cell separation after cytokinesis(GO:0000920)
0.1 0.3 GO:0043711 pilus organization(GO:0043711)
0.1 0.5 GO:0009438 methylglyoxal metabolic process(GO:0009438) methylglyoxal catabolic process(GO:0051596)
0.1 0.1 GO:0097305 response to alcohol(GO:0097305)
0.1 0.4 GO:1900190 regulation of multi-organism process(GO:0043900) regulation of single-species biofilm formation(GO:1900190)
0.1 0.3 GO:0071229 cellular response to acid chemical(GO:0071229)
0.1 0.2 GO:0015707 nitrite transport(GO:0015707)
0.0 0.2 GO:0046219 tryptophan biosynthetic process(GO:0000162) indole-containing compound biosynthetic process(GO:0042435) indolalkylamine biosynthetic process(GO:0046219) tetrahydrofolate biosynthetic process(GO:0046654)
0.0 0.1 GO:0042176 negative regulation of catabolic process(GO:0009895) regulation of protein catabolic process(GO:0042176) negative regulation of protein catabolic process(GO:0042177)
0.0 0.4 GO:0034219 carbohydrate transmembrane transport(GO:0034219)
0.0 0.1 GO:0010043 response to zinc ion(GO:0010043)
0.0 0.7 GO:0072329 monocarboxylic acid catabolic process(GO:0072329)
0.0 0.1 GO:0006284 base-excision repair(GO:0006284)
0.0 0.0 GO:0015827 tryptophan transport(GO:0015827)
0.0 0.4 GO:0031669 cellular response to nutrient levels(GO:0031669)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.5 GO:0031225 anchored component of membrane(GO:0031225)
0.1 0.2 GO:0005950 anthranilate synthase complex(GO:0005950)
0.1 0.3 GO:0032153 cell division site(GO:0032153)
0.1 0.5 GO:0031246 intrinsic component of periplasmic side of cell outer membrane(GO:0031246)
0.0 0.3 GO:0098533 ATP-binding cassette (ABC) transporter complex(GO:0043190) ATPase dependent transmembrane transport complex(GO:0098533) ATPase complex(GO:1904949)
0.0 0.3 GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing(GO:0055052)
0.0 2.8 GO:0005887 integral component of plasma membrane(GO:0005887)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.5 1.6 GO:0035251 UDP-glucosyltransferase activity(GO:0035251)
0.5 1.5 GO:0015199 amino-acid betaine transmembrane transporter activity(GO:0015199) quaternary ammonium group transmembrane transporter activity(GO:0015651)
0.5 1.9 GO:0003867 4-aminobutyrate transaminase activity(GO:0003867)
0.4 2.9 GO:0016744 transferase activity, transferring aldehyde or ketonic groups(GO:0016744)
0.2 0.7 GO:0015101 organic cation transmembrane transporter activity(GO:0015101)
0.2 0.5 GO:0004033 aldo-keto reductase (NADP) activity(GO:0004033)
0.1 0.3 GO:0015927 trehalase activity(GO:0015927)
0.1 0.3 GO:0004096 catalase activity(GO:0004096)
0.1 1.6 GO:0016831 carboxy-lyase activity(GO:0016831)
0.1 0.5 GO:0003681 bent DNA binding(GO:0003681)
0.1 0.4 GO:0004029 aldehyde dehydrogenase (NAD) activity(GO:0004029)
0.1 0.5 GO:0030955 potassium ion binding(GO:0030955)
0.1 0.3 GO:0016868 intramolecular transferase activity, phosphotransferases(GO:0016868)
0.1 1.1 GO:0016830 carbon-carbon lyase activity(GO:0016830)
0.1 0.2 GO:0015113 nitrite transmembrane transporter activity(GO:0015113)
0.0 0.1 GO:0019104 DNA N-glycosylase activity(GO:0019104)
0.0 0.3 GO:0008483 transaminase activity(GO:0008483)
0.0 0.7 GO:0016836 hydro-lyase activity(GO:0016836)
0.0 0.1 GO:0043856 anti-sigma factor antagonist activity(GO:0043856)
0.0 0.1 GO:0051920 peroxiredoxin activity(GO:0051920)
0.0 0.1 GO:0052621 diguanylate cyclase activity(GO:0052621)
0.0 0.0 GO:0015196 L-phenylalanine transmembrane transporter activity(GO:0015192) L-tryptophan transmembrane transporter activity(GO:0015196)
0.0 0.1 GO:0016881 acid-amino acid ligase activity(GO:0016881)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.1 REACTOME HEMOSTASIS Genes involved in Hemostasis