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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for Sigma24

Z-value: 1.03

Transcription factors associated with Sigma24

Gene Symbol Gene ID Gene Info
rpoE
rpoE RNA polymerase sigma factor RpoE

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
rpoE0.772.7e-02Click!

Activity profile of Sigma24 motif

Sorted Z-values of Sigma24 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
bamD 3.37
bamD
Outer Membrane Protein Assembly Complex - BamD subunit
micL 3.27
micL
MicL-S small regulatory RNA
fusA-tufA 2.86
tufA
fusA
elongation factor Tu
elongation factor G
lpxD 2.55
lpxD
UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase
cyaR 2.21
cyaR
CyaR
bamA 2.21
bamA
Outer Membrane Protein Assembly Complex - BamA subunit
hcp-hcr 2.17
hcr
hcp
NADH oxidoreductase
hybrid-cluster protein
bamE 2.00
bamE
Outer Membrane Protein Assembly Complex - BamE subunit
ahpF 1.83
ahpF
alkyl hydroperoxide reductase, AhpF component
ybaB-recR 1.82
ybaB
recR
conserved DNA-binding protein
recombination and repair
lptD-surA-pdxA 1.63
lptD
pdxA
surA
outer membrane lipopolysaccharide transport and assembly complex - LptD subunit
4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent
peptidyl-prolyl cis-trans isomerase (PPIase)
dsbC-recJ-prfB 1.59
recJ
dsbC
prfB
ssDNA-specific exonuclease RecJ
protein disulfide isomerase/protein disulfide oxidoreductase - DsbCreduced
peptide chain release factor RF2
clpX-lon 1.57
clpX
lon
ClpX
DNA-binding, ATP-dependent protease La
bamC 1.54
bamC
Outer Membrane Protein Assembly Complex - BamC subunit
dsbC 1.53
dsbC
protein disulfide isomerase/protein disulfide oxidoreductase - DsbCreduced
surA-pdxA-rsmA-apaGH 1.43
apaG
pdxA
rsmA
apaH
surA
hypothetical protein
4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent
16S rRNA m62A1518,m62A1519 dimethyltransferase
diadenosine tetraphosphatase
peptidyl-prolyl cis-trans isomerase (PPIase)
yfeYX 1.42
yfeX
yfeY
porphyrinogen peroxidase
predicted outer membrane lipoprotein
lptB-rpoN-hpf-ptsN-rapZ 1.35
rapZ
ptsN
rpoN
lptB
hpf
RNase adaptor protein
phosphotransferase system enzyme IIA, regulation of potassium transport
RNA polymerase, sigma 54 (sigma N) factor
LptB
hibernation promoting factor
rseP 1.29
rseP
intramembrane zinc metalloprotease, signal peptide peptidase
lptAB 1.28
lptA
lptB
LptA
LptB
skp-lpxD-fabZ-lpxA 1.15
lpxA
lpxD
skp
fabZ
UDP-N-acetylglucosamine acyltransferase
UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase
periplasmic chaperone
3-hydroxy-acyl-[acyl-carrier-protein] dehydratase
degP 1.14
degP
serine protease Do
plsB 1.12
plsB
glycerol-3-phosphate acyltransferase
rpoD 1.05
rpoD
RNA polymerase, sigma 70 (sigma D) factor
rybB 1.03
rybB
RybB
yeaY 1.00
yeaY
predicted lipoprotein
malQ 0.99
malQ
amylomaltase/amylomaltase/amylomaltase
bamB-der 0.91
der
bamB
50S ribosomal subunit stability factor
Outer Membrane Protein Assembly Complex - BamB subunit
greA 0.89
greA
transcription elongation factor GreA
bamA-skp-lpxD-fabZ-lpxAB-rnhB-dnaE 0.86
skp
rnhB
lpxA
lpxB
lpxD
bamA
fabZ
dnaE
periplasmic chaperone
RNAse HII, degrades RNA of DNA-RNA hybrids
UDP-N-acetylglucosamine acyltransferase
lipid A disaccharide synthase
UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase
Outer Membrane Protein Assembly Complex - BamA subunit
3-hydroxy-acyl-[acyl-carrier-protein] dehydratase
DNA polymerase III, α subunit
yraP 0.81
yraP
lipoprotein
rutR 0.79
rutR
RutR DNA-binding transcriptional dual regulator
rseABC 0.62
rseB
rseC
rseA
rseB
protein RseC
anti-sigma factor
bepA-yfgD 0.57
yfgD
bepA
predicted oxidoreductase
chaperone/protease involved in the maintenance of OM integrity
fkpA 0.49
fkpA
peptidyl-prolyl cis-trans isomerase; in protein folding
ibaG 0.37
ibaG
predicted DNA-binding transcriptional regulator
ytfJ 0.21
ytfJ
conserved protein
ygiM-cca 0.19
cca
ygiM
fused tRNA nucleotidyltransferase / 2',3'-cyclic phosphodiesterase / 2' nucleotidase and phosphatase
predicted signal transduction protein (SH3 domain)
ygiM 0.12
ygiM
predicted signal transduction protein (SH3 domain)

Network of associatons between targets according to the STRING database.

First level regulatory network of Sigma24

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
1.5 10.5 GO:0051205 protein insertion into membrane(GO:0051205)
0.9 4.6 GO:0071709 cell envelope organization(GO:0043163) Gram-negative-bacterium-type cell outer membrane assembly(GO:0043165) membrane biogenesis(GO:0044091) membrane assembly(GO:0071709)
0.7 2.2 GO:0046209 nitric oxide metabolic process(GO:0046209) nitric oxide catabolic process(GO:0046210)
0.7 2.6 GO:0015920 lipopolysaccharide transport(GO:0015920)
0.5 2.7 GO:0006515 misfolded or incompletely synthesized protein catabolic process(GO:0006515)
0.4 1.6 GO:0006415 translational termination(GO:0006415) cellular protein complex disassembly(GO:0043624)
0.4 1.8 GO:0071897 DNA synthesis involved in DNA repair(GO:0000731) DNA biosynthetic process(GO:0071897)
0.2 2.2 GO:0046493 lipid A biosynthetic process(GO:0009245) lipid A metabolic process(GO:0046493)
0.2 0.5 GO:0042026 protein refolding(GO:0042026)
0.1 1.0 GO:0046352 disaccharide catabolic process(GO:0046352)
0.1 0.2 GO:0031123 RNA 3'-end processing(GO:0031123)
0.0 0.6 GO:0061077 chaperone-mediated protein folding(GO:0061077)
0.0 0.3 GO:0006644 phospholipid metabolic process(GO:0006644) phospholipid biosynthetic process(GO:0008654)
0.0 0.8 GO:0009408 response to heat(GO:0009408)
0.0 0.8 GO:0045893 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)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.6 10.9 GO:1990063 Bam protein complex(GO:1990063)
0.1 1.3 GO:0098533 ATP-binding cassette (ABC) transporter complex(GO:0043190) ATPase dependent transmembrane transport complex(GO:0098533) ATPase complex(GO:1904949)
0.1 10.0 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)
0.0 11.4 GO:0005829 cytosol(GO:0005829)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.8 3.1 GO:0050570 4-hydroxythreonine-4-phosphate dehydrogenase activity(GO:0050570)
0.7 2.0 GO:0008693 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity(GO:0008693) 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity(GO:0019171) 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity(GO:0047451)
0.7 2.6 GO:0032403 lipopolysaccharide transmembrane transporter activity(GO:0015221) lipopolysaccharide-transporting ATPase activity(GO:0015437) protein complex binding(GO:0032403)
0.6 1.9 GO:0045152 antisigma factor binding(GO:0045152)
0.6 1.8 GO:0070402 NADPH binding(GO:0070402)
0.5 1.6 GO:0008409 single-stranded DNA exodeoxyribonuclease activity(GO:0008297) 5'-3' exonuclease activity(GO:0008409)
0.4 3.6 GO:0016684 peroxidase activity(GO:0004601) oxidoreductase activity, acting on peroxide as acceptor(GO:0016684)
0.4 2.7 GO:0004252 serine-type endopeptidase activity(GO:0004252)
0.3 1.0 GO:0004133 glycogen debranching enzyme activity(GO:0004133)
0.3 1.5 GO:0016864 protein disulfide isomerase activity(GO:0003756) intramolecular oxidoreductase activity, transposing S-S bonds(GO:0016864)
0.3 0.9 GO:0001098 basal transcription machinery binding(GO:0001098) bacterial-type RNA polymerase holo enzyme binding(GO:0001108)
0.3 2.5 GO:0016410 N-acyltransferase activity(GO:0016410)
0.2 1.1 GO:0008374 O-acyltransferase activity(GO:0008374)
0.2 0.9 GO:0097216 guanosine tetraphosphate binding(GO:0097216)
0.2 0.8 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)
0.1 0.2 GO:0070567 cytidylyltransferase activity(GO:0070567)
0.1 0.6 GO:0008237 metallopeptidase activity(GO:0008237)
0.0 0.8 GO:0000976 transcription regulatory region sequence-specific DNA binding(GO:0000976)
0.0 1.8 GO:0003677 DNA binding(GO:0003677)
0.0 5.0 GO:0005515 protein binding(GO:0005515)