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

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Results for Sigma24

Z-value: 2.39

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
rpoE0.922.1e-11Click!

Activity profile of Sigma24 motif

Sorted Z-values of Sigma24 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
yraP 42.96
yraP
lipoprotein
fusA-tufA 35.77
tufA
fusA
elongation factor Tu
elongation factor G
bamA-skp-lpxD-fabZ-lpxAB-rnhB-dnaE 22.99
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
bamD 22.94
bamD
Outer Membrane Protein Assembly Complex - BamD subunit
malQ 20.83
malQ
amylomaltase/amylomaltase/amylomaltase
ybaB-recR 19.32
ybaB
recR
conserved DNA-binding protein
recombination and repair
bamA 19.15
bamA
Outer Membrane Protein Assembly Complex - BamA subunit
fkpA 19.04
fkpA
peptidyl-prolyl cis-trans isomerase; in protein folding
bamB-der 17.73
der
bamB
50S ribosomal subunit stability factor
Outer Membrane Protein Assembly Complex - BamB subunit
skp-lpxD-fabZ-lpxA 17.64
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
lptB-rpoN-hpf-ptsN-rapZ 17.30
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
bamC 16.66
bamC
Outer Membrane Protein Assembly Complex - BamC subunit
lptD-surA-pdxA 16.33
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)
degP 15.98
degP
serine protease Do
lpxD 15.47
lpxD
UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase
surA-pdxA-rsmA-apaGH 15.06
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)
rseP 14.28
rseP
intramembrane zinc metalloprotease, signal peptide peptidase
greA 13.22
greA
transcription elongation factor GreA
lpxP 12.79
lpxP
palmitoleoyl acyltransferase
ygiM-cca 10.62
cca
ygiM
fused tRNA nucleotidyltransferase / 2',3'-cyclic phosphodiesterase / 2' nucleotidase and phosphatase
predicted signal transduction protein (SH3 domain)
psd-mscM 10.01
mscM
psd
mechanosensitive channel of miniconductance MscM
phosphatidylserine decarboxylase, proenzyme
bepA-yfgD 9.94
yfgD
bepA
predicted oxidoreductase
chaperone/protease involved in the maintenance of OM integrity
yfeYX 9.87
yfeX
yfeY
porphyrinogen peroxidase
predicted outer membrane lipoprotein
rfaD-waaFCL 9.84
waaC
waaF
waaL
rfaD
ADP-heptose:LPS heptosyltransferase I
ADP-heptose:LPS heptosyltransferase II
O-antigen ligase
ADP-L-glycero-D-mannoheptose-6-epimerase
dsbC-recJ-prfB 9.55
recJ
dsbC
prfB
ssDNA-specific exonuclease RecJ
protein disulfide isomerase/protein disulfide oxidoreductase - DsbCreduced
peptide chain release factor RF2
bacA 9.42
bacA
undecaprenyl pyrophosphate phosphatase
yfeKS 8.80
yfeK
yfeS
predicted protein
conserved protein
sbmA-yaiW 8.21
sbmA
yaiW
peptide antibiotic / peptide nucleic acid transporter
surface exposed outer membrane lipoprotein
clpX-lon 8.10
clpX
lon
ClpX
DNA-binding, ATP-dependent protease La
lptAB 8.09
lptA
lptB
LptA
LptB
phoQ 6.40
phoQ
PhoQ sensory histidine kinase
ahpF 5.97
ahpF
alkyl hydroperoxide reductase, AhpF component
ygiM 5.86
ygiM
predicted signal transduction protein (SH3 domain)
plsB 5.73
plsB
glycerol-3-phosphate acyltransferase
ibaG 4.96
ibaG
predicted DNA-binding transcriptional regulator
yhjJ 4.91
yhjJ
predicted zinc-dependent peptidase
yieEF 4.86
yieE
yieF
predicted phosphopantetheinyl transferase
chromate reductase
yqjA-mzrA 2.86
yqjA
mzrA
membrane transport protein; required for proton-motive force (PMF) dependent drug efflux
MzrA
rseABC 2.73
rseB
rseC
rseA
rseB
protein RseC
anti-sigma factor
yggN 1.51
yggN
predicted protein
rpoH 1.17
rpoH
RNA polymerase, sigma 32 (sigma H) factor
eptB 0.60
eptB
Kdo2-lipid A phosphoethanolamine 7''-transferase
micL 0.25
micL
MicL-S small regulatory RNA

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
14.3 100.4 GO:0051205 protein insertion into membrane(GO:0051205)
9.6 48.0 GO:0043165 cell envelope organization(GO:0043163) Gram-negative-bacterium-type cell outer membrane assembly(GO:0043165) membrane biogenesis(GO:0044091) membrane assembly(GO:0071709)
6.3 19.0 GO:0042026 protein refolding(GO:0042026)
6.3 25.4 GO:0015920 lipopolysaccharide transport(GO:0015920)
5.0 10.0 GO:0071470 cellular response to osmotic stress(GO:0071470)
4.8 24.1 GO:0006515 misfolded or incompletely synthesized protein catabolic process(GO:0006515)
3.9 19.3 GO:0071897 DNA synthesis involved in DNA repair(GO:0000731) DNA biosynthetic process(GO:0071897)
3.5 10.6 GO:0031123 RNA 3'-end processing(GO:0031123)
3.5 10.4 GO:0009244 lipopolysaccharide core region biosynthetic process(GO:0009244) lipopolysaccharide core region metabolic process(GO:0046401)
2.8 28.3 GO:0006643 membrane lipid metabolic process(GO:0006643) glycolipid metabolic process(GO:0006664) glycolipid biosynthetic process(GO:0009247) membrane lipid biosynthetic process(GO:0046467) lipooligosaccharide metabolic process(GO:1901269) lipooligosaccharide biosynthetic process(GO:1901271)
2.7 8.2 GO:0042884 microcin transport(GO:0042884)
2.6 20.8 GO:0046352 disaccharide catabolic process(GO:0046352)
2.4 9.6 GO:0043624 translational termination(GO:0006415) cellular protein complex disassembly(GO:0043624)
2.1 6.4 GO:0010350 cellular response to magnesium starvation(GO:0010350)
0.7 9.9 GO:0061077 chaperone-mediated protein folding(GO:0061077)
0.6 5.7 GO:0008654 phospholipid metabolic process(GO:0006644) phospholipid biosynthetic process(GO:0008654)
0.6 4.9 GO:0071466 xenobiotic metabolic process(GO:0006805) response to xenobiotic stimulus(GO:0009410) cellular response to xenobiotic stimulus(GO:0071466)
0.6 9.4 GO:0000270 peptidoglycan metabolic process(GO:0000270) aminoglycan metabolic process(GO:0006022) glycosaminoglycan metabolic process(GO:0030203)
0.4 2.9 GO:0031399 regulation of protein modification process(GO:0031399)
0.3 1.2 GO:0001121 transcription from bacterial-type RNA polymerase promoter(GO:0001121)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
14.2 99.4 GO:1990063 Bam protein complex(GO:1990063)
1.1 17.3 GO:0022627 small ribosomal subunit(GO:0015935) cytosolic small ribosomal subunit(GO:0022627)
1.0 100.9 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)
0.3 139.4 GO:0005829 cytosol(GO:0005829)
0.2 22.0 GO:0005887 integral component of plasma membrane(GO:0005887)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
13.5 40.6 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)
7.8 31.4 GO:0050570 4-hydroxythreonine-4-phosphate dehydrogenase activity(GO:0050570)
6.9 20.8 GO:0004133 glycogen debranching enzyme activity(GO:0004133)
6.3 25.4 GO:0032403 lipopolysaccharide transmembrane transporter activity(GO:0015221) lipopolysaccharide-transporting ATPase activity(GO:0015437) protein complex binding(GO:0032403)
5.7 17.0 GO:0045152 antisigma factor binding(GO:0045152)
4.4 13.2 GO:0001108 basal transcription machinery binding(GO:0001098) bacterial-type RNA polymerase holo enzyme binding(GO:0001108)
3.5 17.7 GO:0097216 guanosine tetraphosphate binding(GO:0097216)
3.5 10.6 GO:0070567 cytidylyltransferase activity(GO:0070567)
3.4 24.1 GO:0004252 serine-type endopeptidase activity(GO:0004252)
3.3 10.0 GO:0022836 gated channel activity(GO:0022836)
3.2 9.6 GO:0008297 single-stranded DNA exodeoxyribonuclease activity(GO:0008297) 5'-3' exonuclease activity(GO:0008409)
3.1 9.4 GO:0050380 undecaprenyl-diphosphatase activity(GO:0050380)
2.7 8.2 GO:0019534 toxin transporter activity(GO:0019534)
2.5 9.9 GO:0020037 heme binding(GO:0020037)
2.4 4.9 GO:0008897 holo-[acyl-carrier-protein] synthase activity(GO:0008897)
2.0 6.0 GO:0070402 NADPH binding(GO:0070402)
1.7 15.5 GO:0016410 N-acyltransferase activity(GO:0016410)
1.4 9.8 GO:0050661 NADP binding(GO:0050661)
1.0 5.7 GO:0008374 O-acyltransferase activity(GO:0008374)
0.9 9.9 GO:0008237 metallopeptidase activity(GO:0008237)
0.6 12.8 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups(GO:0016747)
0.3 6.4 GO:0000155 phosphorelay sensor kinase activity(GO:0000155) protein histidine kinase activity(GO:0004673)
0.3 0.6 GO:0016780 phosphotransferase activity, for other substituted phosphate groups(GO:0016780)
0.3 19.3 GO:0003677 DNA binding(GO:0003677)
0.3 2.9 GO:0019899 enzyme binding(GO:0019899)
0.2 67.2 GO:0005515 protein binding(GO:0005515)