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

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Results for Sigma38

Z-value: 3.03

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-0.661.7e-04Click!

Activity profile of Sigma38 motif

Sorted Z-values of Sigma38 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
glgS 48.05
glgS
surface composition regulator
ryjA 44.75
ryjA
RyjA
wrbA-yccJ 26.13
wrbA
yccJ
NAD(P)H:quinone oxidoreductase
predicted protein
uspB 24.80
uspB
predicted universal stress (ethanol tolerance) protein B
osmB 22.36
osmB
OsmB osmotically inducible lipoprotein
patA 21.51
patA
putrescine aminotransferase
ecnB 17.54
ecnB
bacteriolytic entericidin B lipoprotein
sdsR 17.15
sdsR
RyeB
astCADBE 16.53
astA
astB
astC
astD
astE
arginine succinyltransferase
succinylarginine dihydrolase
succinylornithine transaminase
aldehyde dehydrogenase
succinylglutamate desuccinylase
ytfK 15.90
ytfK
conserved protein
poxB 14.87
poxB
pyruvate oxidase
ydcSTUV-patD 14.58
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
hmp 14.57
hmp
nitric oxide dioxygenase
treF 13.69
treF
cytoplasmic trehalase
yiaG 13.60
yiaG
predicted transcriptional regulator
bolA 13.60
bolA
BolA DNA-binding transcriptional dual regulator
blc 13.57
blc
outer membrane lipoprotein (lipocalin)
dgcC 12.85
dgcC
diguanylate cyclase
gadE 11.95
gadE
GadE DNA-binding transcriptional activator
yggE 11.17
yggE
conserved protein
yhfG-fic-pabA 10.96
fic
pabA
yhfG
stationary-phase protein
aminodeoxychorismate synthase component 2
predicted protein
ybiI 10.77
ybiI
conserved protein
sodC 10.34
sodC
superoxide dismutase (Cu-Zn)
treA 9.91
treA
periplasmic trehalase
narU 9.90
narU
nitrate / nitrite transporter NarU
fbaB 9.74
fbaB
fructose bisphosphate aldolase class I
pdeC 9.64
pdeC
predicted c-di-GMP-specific phosphodiesterase
tam 9.63
tam
trans-aconitate 2-methyltransferase
yadV-htrE 9.38
htrE
yadV
putative outer membrane usher protein
probable pilin chaperone similar to PapD
dkgA 9.37
dkgA
methylglyoxal reductase/isobutyraldehyde reductase/β-keto ester reductase/2,5-diketo-D-gluconate reductase
kbp 9.31
kbp
K+ binding protein
asr 9.11
asr
acid shock protein
yeiL 8.75
yeiL
YeiL DNA-binding transcriptional activator
ldcC 8.63
ldcC
lysine decarboxylase 2
aldB 8.63
aldB
acetaldehyde dehydrogenase
yhjG 8.62
yhjG
predicted outer membrane biogenesis protein
fumC 8.44
fumC
fumarase C
yddG 8.19
yddG
aromatic amino acid exporter
bsmA 7.85
bsmA
conserved protein
otsBA 7.83
otsA
otsB
trehalose-6-phosphate synthase
trehalose-6-phosphate phosphatase
talA-tktB 7.80
talA
tktB
transaldolase A
transketolase II
gabDTP 7.71
gabD
gabT
gabP
succinate-semialdehyde dehydrogenase (NADP+)
4-aminobutyrate aminotransferase
4-aminobutyrate:H+ symporter
msyB 7.63
msyB
acidic protein that suppresses heat sensitivity of a secY mutant
ssrS 7.24
ssrS
6S RNA
ssrS-fau 7.23
ssrS
fau
6S RNA
5-formyltetrahydrofolate cyclo-ligase
iraD 7.18
iraD
inhibitor of σS proteolysis
insC-5CD-5D-5-yqiGHI 7.17
insCD-5
yqiG
yqiI
yqiH
insC-5
IS2 element transposase InsAB'
predicted outer membrane usher protein
protein involved in detoxification of methylglyoxal
predicted periplasmic pilin chaperone
IS2 insertion element repressor InsA
ydbD 7.17
ydbD
protein involved in detoxification of methylglyoxal
gadBC 7.10
gadB
gadC
glutamate decarboxylase B subunit
glutamic acid:4-aminobutyrate antiporter
otsA 7.07
otsA
trehalose-6-phosphate synthase
dhaR 5.95
dhaR
DhaR DNA-binding transcriptional dual regulator
ybjP 5.91
ybjP
predicted lipoprotein
lsrACDBFG-tam 5.80
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
cbpAM 5.70
cbpM
cbpA
chaperone modulator protein CbpM
chaperone with DnaK; curved DNA-binding protein
rssB 5.61
rssB
regulator of RpoS
katE 5.20
katE
catalase II
araFGH 5.07
araF
araG
araH
arabinose ABC transporter - periplasmic binding protein
arabinose ABC transporter - ATP binding subunit
arabinose ABC transporter - membrane subunit
cfa 5.06
cfa
cyclopropane fatty acyl phospholipid synthase
csrA 4.49
csrA
carbon storage regulator; pleiotropic regulatory protein for carbon source metabolism
acnA 4.45
acnA
aconitate hydratase 1
ada-alkB 4.45
alkB
ada
AlkB repair system for alkylated DNA and RNA
Ada DNA-binding transcriptional dual regulator / DNA repair protein
gadX 3.83
gadX
GadX DNA-binding transcriptional dual regulator
yhiM 3.60
yhiM
inner membrane protein with a role in acid resistance
insN-1I-1O-1 3.57
insI-1
insO-1
insN-1
transposase of IS30
CP4-6 prophage; partial transposase of insertion element IS911A, interrupted by insertion of IS30 element
CP4-6 prophage; partial regulator of insertion element IS911A
tktB 3.53
tktB
transketolase II
ybgA-phr 3.20
ybgA
phr
conserved protein
deoxyribodipyrimidine photolyase (photoreactivation)
ydhYVWXUT 3.17
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
ycgZ-ymgA-ariR-ymgC 3.02
ariR
ymgC
ymgA
ycgZ
regulator of acid resistance, influenced by indole
protein involved in biofilm formation
protein involved in biofilm formation
predicted protein
osmF-yehYXW 2.99
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
gadXW 2.87
gadW
gadX
GadW DNA-binding transcriptional dual regulator
GadX DNA-binding transcriptional dual regulator
yciG 2.80
yciG
predicted protein
fadL 2.57
fadL
long-chain fatty acid outer membrane porin; bacteriophage T2 receptor
osmC 2.49
osmC
osmotically inducible peroxiredoxin
dkgB 2.27
dkgB
methylglyoxal reductase/4-nitrobenzaldehyde reductase/2,5-diketo-D-gluconate reductase
pykF 2.16
pykF
pyruvate kinase I
csgDEFG 2.11
csgG
csgF
csgE
csgD
curli secretion channel
curli assembly component
curli transport specificity factor
CsgD DNA-binding transcriptional dual regulator
appY 2.05
appY
AppY DNA-binding transcriptional activator
hdeAB-yhiD 2.04
yhiD
hdeB
hdeA
inner membrane protein YhiD
HdeB monomer
HdeA monomer, chaperone active form
csiD-lhgO-gabDTP 1.94
gabD
lhgO
gabP
csiD
gabT
succinate-semialdehyde dehydrogenase (NADP+)
L-2-hydroxyglutarate oxidase
4-aminobutyrate:H+ symporter
predicted protein
4-aminobutyrate aminotransferase
ansP 1.17
ansP
L-asparagine transporter
ddpXABCDF 0.91
ddpX
ddpD
ddpF
ddpA
ddpB
ddpC
D-Ala-D-Ala dipeptidase
YddP
YddO
YddS
YddR
YddQ
yciGFE 0.60
yciG
yciF
yciE
predicted protein
conserved protein
conserved protein
hofMNOP 0.52
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
gadE-mdtEF 0.48
mdtF
mdtE
gadE
MdtEF-TolC multidrug efflux pump - permease subunit
MdtEF-TolC multidrug efflux pump - membrane fusion protein
GadE DNA-binding transcriptional activator
ihfA 0.00
ihfA
integration host factor (IHF), α subunit

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
16.7 33.4 GO:0097305 response to alcohol(GO:0097305)
16.0 48.0 GO:1900232 regulation of single-species biofilm formation on inanimate substrate(GO:1900231) negative regulation of single-species biofilm formation on inanimate substrate(GO:1900232)
8.9 26.6 GO:0071474 cellular hyperosmotic response(GO:0071474)
5.5 16.5 GO:0006527 succinate metabolic process(GO:0006105) arginine catabolic process(GO:0006527)
5.0 14.9 GO:0005991 trehalose metabolic process(GO:0005991)
4.9 14.6 GO:0046210 nitric oxide metabolic process(GO:0046209) nitric oxide catabolic process(GO:0046210)
4.1 16.6 GO:0043711 pilus organization(GO:0043711)
3.4 10.3 GO:0006801 superoxide metabolic process(GO:0006801)
3.3 9.9 GO:0015707 nitrite transport(GO:0015707)
3.0 18.2 GO:0009396 folic acid-containing compound biosynthetic process(GO:0009396) pteridine-containing compound biosynthetic process(GO:0042559)
3.0 3.0 GO:1900191 negative regulation of multi-organism process(GO:0043901) negative regulation of single-species biofilm formation(GO:1900191)
2.9 8.6 GO:0051223 regulation of protein localization(GO:0032880) regulation of protein transport(GO:0051223) regulation of establishment of protein localization(GO:0070201)
2.8 8.4 GO:0006108 malate metabolic process(GO:0006108)
2.7 8.2 GO:0015827 tryptophan transport(GO:0015827)
2.6 7.8 GO:0042542 response to hydrogen peroxide(GO:0042542)
2.6 5.2 GO:0072593 reactive oxygen species metabolic process(GO:0072593)
2.4 14.6 GO:0015931 nucleobase-containing compound transport(GO:0015931)
2.4 9.7 GO:0042450 ornithine metabolic process(GO:0006591) arginine biosynthetic process via ornithine(GO:0042450)
2.4 7.2 GO:0009895 negative regulation of catabolic process(GO:0009895) regulation of protein catabolic process(GO:0042176) negative regulation of protein catabolic process(GO:0042177)
2.2 11.2 GO:0034614 cellular response to reactive oxygen species(GO:0034614)
2.2 4.4 GO:0044728 DNA methylation or demethylation(GO:0044728)
2.2 6.5 GO:1901654 response to methylglyoxal(GO:0051595) response to ketone(GO:1901654)
1.9 11.6 GO:0009438 methylglyoxal metabolic process(GO:0009438) methylglyoxal catabolic process(GO:0051596)
1.9 11.3 GO:0009052 pentose-phosphate shunt, non-oxidative branch(GO:0009052)
1.7 5.1 GO:0042882 L-arabinose transport(GO:0042882)
1.5 9.1 GO:0010043 response to zinc ion(GO:0010043)
1.5 4.5 GO:0010906 regulation of glucose metabolic process(GO:0010906)
1.5 4.4 GO:0006097 glyoxylate cycle(GO:0006097)
1.5 39.2 GO:0051289 protein tetramerization(GO:0051262) protein homotetramerization(GO:0051289)
1.2 8.6 GO:0009068 aspartate family amino acid catabolic process(GO:0009068)
1.1 2.1 GO:1900190 regulation of multi-organism process(GO:0043900) regulation of single-species biofilm formation(GO:1900190)
0.7 4.5 GO:0030162 regulation of proteolysis(GO:0030162)
0.7 3.6 GO:0071229 cellular response to acid chemical(GO:0071229)
0.7 2.0 GO:0071468 cellular response to acidic pH(GO:0071468)
0.6 3.4 GO:0071978 bacterial-type flagellum-dependent swarming motility(GO:0071978)
0.4 5.1 GO:0030258 lipid modification(GO:0030258)
0.3 3.0 GO:0006869 lipid transport(GO:0006869)
0.3 2.1 GO:0016036 cellular response to phosphate starvation(GO:0016036)
0.2 0.7 GO:0051454 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)
0.2 2.5 GO:1901700 response to oxygen-containing compound(GO:1901700)
0.2 0.5 GO:0015976 carbon utilization(GO:0015976)
0.1 0.9 GO:0006023 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
4.4 17.5 GO:0031225 anchored component of membrane(GO:0031225)
3.7 11.0 GO:0005950 anthranilate synthase complex(GO:0005950)
1.0 11.2 GO:0071575 integral component of external side of plasma membrane(GO:0071575)
0.2 2.1 GO:0031246 intrinsic component of periplasmic side of cell outer membrane(GO:0031246)
0.0 3.8 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
7.9 23.6 GO:0015927 trehalase activity(GO:0015927)
6.6 39.7 GO:0004029 aldehyde dehydrogenase (NAD) activity(GO:0004029)
5.2 26.1 GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor(GO:0016655)
5.0 14.9 GO:0035251 UDP-glucosyltransferase activity(GO:0035251)
4.8 9.7 GO:0004777 succinate-semialdehyde dehydrogenase (NAD+) activity(GO:0004777)
3.9 11.6 GO:0004033 aldo-keto reductase (NADP) activity(GO:0004033)
3.8 19.0 GO:0051213 dioxygenase activity(GO:0051213)
3.4 10.3 GO:0016721 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
3.3 9.9 GO:0015113 nitrite transmembrane transporter activity(GO:0015113)
3.2 9.7 GO:0004332 fructose-bisphosphate aldolase activity(GO:0004332)
3.2 12.8 GO:0052621 diguanylate cyclase activity(GO:0052621)
2.7 8.2 GO:0015192 L-phenylalanine transmembrane transporter activity(GO:0015192) L-tryptophan transmembrane transporter activity(GO:0015196)
1.8 7.2 GO:0016882 cyclo-ligase activity(GO:0016882)
1.8 7.2 GO:0043856 anti-sigma factor antagonist activity(GO:0043856)
1.8 8.9 GO:0071111 cyclic-guanylate-specific phosphodiesterase activity(GO:0071111)
1.7 5.2 GO:0004096 catalase activity(GO:0004096)
1.7 5.1 GO:0015147 L-arabinose transmembrane transporter activity(GO:0015147)
1.7 8.4 GO:0004333 fumarate hydratase activity(GO:0004333)
1.6 11.3 GO:0016744 transferase activity, transferring aldehyde or ketonic groups(GO:0016744)
1.3 2.6 GO:0005216 ion channel activity(GO:0005216)
1.2 9.3 GO:0030955 potassium ion binding(GO:0030955)
0.9 4.5 GO:0048027 mRNA 5'-UTR binding(GO:0048027)
0.8 2.5 GO:0051920 peroxiredoxin activity(GO:0051920)
0.8 5.7 GO:0003681 bent DNA binding(GO:0003681)
0.7 2.0 GO:0051087 chaperone binding(GO:0051087)
0.6 3.0 GO:0019829 cation-transporting ATPase activity(GO:0019829)
0.6 14.9 GO:0050660 flavin adenine dinucleotide binding(GO:0050660)
0.5 7.3 GO:0008483 transaminase activity(GO:0008483)
0.5 5.8 GO:0015145 monosaccharide transmembrane transporter activity(GO:0015145)
0.4 2.9 GO:0001140 transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding(GO:0001140) bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding(GO:0001216)
0.4 8.3 GO:0016831 carboxy-lyase activity(GO:0016831)
0.3 4.4 GO:0003729 mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.3 4.5 GO:0008757 S-adenosylmethionine-dependent methyltransferase activity(GO:0008757)
0.2 0.9 GO:0008235 metalloexopeptidase activity(GO:0008235)
0.2 1.5 GO:0016989 sigma factor antagonist activity(GO:0016989)
0.2 3.2 GO:0016830 carbon-carbon lyase activity(GO:0016830)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
1.5 4.4 PID P73PATHWAY p73 transcription factor network

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
2.4 7.2 REACTOME INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION Genes involved in Influenza Viral RNA Transcription and Replication
1.5 4.4 REACTOME PURINE SALVAGE Genes involved in Purine salvage