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

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Results for IHF

Z-value: 1.00

Transcription factors associated with IHF

Gene Symbol Gene ID Gene Info
infA
infA integration host factor subunit alpha
infB
infB integration host factor subunit beta

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
infA-0.534.3e-03Click!
infB-0.481.1e-02Click!

Activity profile of IHF motif

Sorted Z-values of IHF motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
ilvL 5.92
ilvL
ilvGEDA operon leader peptide
acs-yjcH-actP 5.48
acs
actP
yjcH
acetyl-CoA synthetase (AMP-forming)
acetate / glycolate : cation symporter
conserved inner membrane protein
uspB 5.34
uspB
predicted universal stress (ethanol tolerance) protein B
ilvLXG_1G_2MEDA 4.35
ilvE
ilvX
ilvM
ilvL
ilvG_1
ilvD
ilvG_2
ilvA
branched-chain amino-acid aminotransferase
small protein
acetolactate synthase / acetohydroxybutanoate synthase, regulatory subunit
ilvGEDA operon leader peptide
acetolactate synthase II, large subunit, N-ter fragment (pseudogene)
dihydroxy acid dehydratase
acetolactate synthase II, large subunit, C-ter fragment (pseudogene)
threonine deaminase
glcDEFGBA 4.05
glcD
glcE
glcF
glcG
glcA
glcB
glycolate oxidase, predicted FAD-linked subunit
glycolate oxidase, predicted FAD-binding subunit
glycolate oxidase, predicted iron-sulfur subunit
conserved protein
glycolate / lactate:H+ symporter
malate synthase G
yadV-htrE 4.00
htrE
yadV
putative outer membrane usher protein
probable pilin chaperone similar to PapD
patA 3.85
patA
putrescine aminotransferase
osmY 3.44
osmY
periplasmic chaperone, osmotically induced
ssuEADCB 3.08
ssuE
ssuD
ssuA
ssuC
ssuB
NADPH-dependent FMN reductase
alkanesulfonate monooxygenase, FMNH2-dependent
aliphatic sulfonate ABC transporter - periplasmic binding protein
aliphatic sulfonate ABC transporter - membrane subunit
aliphatic sulfonate ABC transporter - ATP binding subunit
ihfA 2.92
ihfA
integration host factor (IHF), α subunit
ompC 2.90
ompC
outer membrane protein C
dps 2.82
dps
stationary phase nucleoid protein that sequesters iron and protects DNA from damage
folA 2.67
folA
dihydrofolate reductase
aceBAK 2.61
aceK
aceB
aceA
isocitrate dehydrogenase phosphatase / isocitrate dehydrogenase kinase
malate synthase A
isocitrate lyase
narK 2.47
narK
nitrate:nitrite antiporter NarK
paaABCDEFGHIJK 2.15
paaB
paaC
paaA
paaF
paaG
paaD
paaE
paaJ
paaK
paaH
paaI
ring 1,2-phenylacetyl-CoA epoxidase subunit
ring 1,2-phenylacetyl-CoA epoxidase, structural subunit
ring 1,2-phenylacetyl-CoA epoxidase, monooxygenase subunit
predicted 2,3-dehydroadipyl-CoA hydratase
predicted ring 1,2-epoxyphenylacetyl-CoA isomerase (oxepin-CoA forming)
phenylacetate degradation protein
ring 1,2-phenylacetyl-CoA epoxidase, reductase subunit
β-ketoadipyl-CoA thiolase
phenylacetate-CoA ligase
3-hydroxyadipyl-CoA dehydrogenase (NAD+)
phenylacetyl-CoA thioesterase
narGHJI 2.01
narG
narI
narH
narJ
nitrate reductase A, α subunit
nitrate reductase A, γ subunit
nitrate reductase A, β subunit
molybdenum cofactor assembly chaperone subunit (δ subunit) of nitrate reductase 1
yjbE 1.96
yjbE
predicted protein
tyrP 1.94
tyrP
tyrosine:H+ symporter TyrP
atoDAEB 1.80
atoB
atoA
atoD
atoE
acetyl-CoA acetyltransferase
acetyl-CoA:acetoacetyl-CoA transferase, β subunit
acetyl-CoA:acetoacetyl-CoA transferase, α subunit
predicted short chain fatty acid transporter
pstS 1.74
pstS
phosphate ABC transporter - periplasmic binding protein
ibpB 1.72
ibpB
small heat shock protein IbpB
fimAICDFGH 1.72
fimA
fimC
fimD
fimF
fimG
fimH
fimI
major type 1 subunit fimbrin (pilin)
periplasmic chaperone, required for type 1 fimbriae
outer membrane protein; export and assembly of type 1 fimbriae
fimbrial morphology
fimbrial morphology
minor fimbrial subunit, D-mannose specific adhesin
fimbrial protein
osmE 1.72
osmE
osmotically inducible protein OsmE
paaZ 1.71
paaZ
oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase
hipBA 1.71
hipA
hipB
serine/threonine kinase HipA
HipB antitoxin and DNA-binding transcriptional repressor
yjbEFGH 1.65
yjbG
yjbF
yjbE
yjbH
conserved protein
predicted lipoprotein
predicted protein
predicted porin
yeiL 1.64
yeiL
YeiL DNA-binding transcriptional activator
adiA 1.57
adiA
arginine decarboxylase, degradative
sufABCDSE 1.33
sufB
sufC
sufA
sufD
sufE
sufS
SufB component of SufBCD Fe-S cluster scaffold complex
SufC component of SufBCD Fe-S cluster scaffold complex
Fe-S transport protein in Fe-S cluster assembly
SufD component of SufBCD Fe-S cluster scaffold complex
sulfur acceptor for SufS cysteine desulfurase
L-cysteine desulfurase
uspA 1.31
uspA
universal stress global stress response regulator
glmY 1.12
glmY
GlmY
glpTQ 1.11
glpT
glpQ
glycerol-3-phosphate:phosphate antiporter
glycerophosphoryl diester phosphodiesterase, periplasmic
ompR-envZ 1.01
envZ
ompR
EnvZ
OmpR transcriptional dual regulator
yiaKLMNO-lyxK-sgbHUE 0.95
lyxK
sgbH
sgbE
sgbU
yiaK
yiaM
yiaL
yiaO
yiaN
L-xylulose kinase
3-keto-L-gulonate 6-phosphate decarboxylase
L-ribulose-5-phosphate 4-epimerase
predicted L-xylulose 5-phosphate 3-epimerase
2,3-diketo-L-gulonate reductase
2,3-diketo-L-gulonate:Na+ symporter - membrane subunit
conserved protein
2,3-diketo-L-gulonate:Na+ symporter - periplasmic binding protein
2,3-diketo-L-gulonate:Na+ symporter - membrane subunit
pstSCA 0.91
pstS
pstC
pstA
phosphate ABC transporter - periplasmic binding protein
phosphate ABC transporter - membrane subunit
phosphate ABC transporter - membrane subunit
mtr 0.88
mtr
tryptohan / indole:H+ symporter Mtr
ulaG 0.85
ulaG
L-ascorbate 6-phosphate lactonase
dcuD 0.79
dcuD
putative transport protein, C4-dicarboxylate uptake C family
ulaABCDEF 0.75
ulaD
ulaE
ulaF
ulaA
ulaB
ulaC
3-keto-L-gulonate 6-phosphate decarboxylase
L-xylulose 5-phosphate 3-epimerase
L-ribulose 5-phosphate 4-epimerase
L-ascorbate PTS permease - UlaA subunit
L-ascorbate PTS permease - UlaB subunit
L-ascorbate PTS permease - UlaC subunit
ubiCA 0.74
ubiC
ubiA
chorismate lyase
4-hydroxybenzoate octaprenyltransferase
hemF 0.51
hemF
coproporphyrinogen III oxidase
dmsABC 0.50
dmsA
dmsB
dmsC
dimethyl sulfoxide reductase, chain A
dimethyl sulfoxide reductase, chain B
dimethyl sulfoxide reductase, chain C
hycABCDEFGHI 0.41
hycD
hycE
hycF
hycG
hycA
hycB
hycC
hycH
hycI
hydrogenase 3, membrane subunit
hydrogenase 3, large subunit
formate hydrogenlyase complex iron-sulfur protein
hydrogenase 3 and formate hydrogenlyase complex, HycG subunit
regulator of the transcriptional regulator FhlA
hydrogenase 3, Fe-S subunit
hydrogenase 3, membrane subunit
protein required for maturation of hydrogenase 3
hydrogenase 3 maturation protease
rpoH 0.22
rpoH
RNA polymerase, sigma 32 (sigma H) factor
rtcBA 0.20
rtcB
rtcA
RNA-splicing ligase RtcB
RNA 3'-terminal phosphate cyclase
tdcABCDEFG 0.10
tdcE
tdcD
tdcG
tdcF
tdcA
tdcC
tdcB
2-ketobutyrate formate-lyase/pyruvate formate-lyase 4, inactive
propionate kinase
L-serine deaminase III
predicted enamine/imine deaminase
TdcA DNA-binding transcriptional activator
serine / threonine:H+ symporter TdcC
catabolic threonine dehydratase
hypABCDE 0.06
hypE
hypD
hypA
hypC
hypB
hydrogenase maturation protein, carbamoyl dehydratase
HypD, scaffold protein for assembly of the Fe-(CN)2CO cofactor
accessory protein for nickel incorporation into hydrogenase 3
HypC, protein involved in hydrogenase 3 maturation
accessory protein for nickel incorporation into hydrogenase isoenzymes
norVW 0.00
norW
norV
NADH:flavorubredoxin reductase
flavorubredoxin

Network of associatons between targets according to the STRING database.

First level regulatory network of IHF

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
2.7 5.3 GO:0097305 response to alcohol(GO:0097305)
1.8 5.5 GO:0018394 tellurite transport(GO:0015710) peptidyl-lysine acetylation(GO:0018394) post-translational protein modification(GO:0043687)
1.5 10.3 GO:0009099 valine biosynthetic process(GO:0009099)
1.4 5.7 GO:0043711 pilus organization(GO:0043711)
1.3 6.7 GO:0046487 glyoxylate metabolic process(GO:0046487)
1.2 3.6 GO:0046379 extracellular polysaccharide biosynthetic process(GO:0045226) extracellular polysaccharide metabolic process(GO:0046379)
1.0 3.1 GO:0009970 cellular response to sulfate starvation(GO:0009970) xenobiotic transport(GO:0042908)
1.0 4.0 GO:0015748 organophosphate ester transport(GO:0015748)
1.0 3.9 GO:0042178 xenobiotic catabolic process(GO:0042178)
0.9 1.8 GO:0019626 short-chain fatty acid catabolic process(GO:0019626)
0.7 2.0 GO:0071941 nitrogen cycle metabolic process(GO:0071941)
0.6 3.8 GO:0009447 polyamine catabolic process(GO:0006598) putrescine catabolic process(GO:0009447)
0.5 1.6 GO:0015707 nitrite transport(GO:0015707)
0.5 2.7 GO:0046654 tetrahydrofolate biosynthetic process(GO:0046654)
0.5 1.6 GO:0006527 arginine catabolic process(GO:0006527)
0.5 2.5 GO:0010921 regulation of phosphatase activity(GO:0010921)
0.3 1.7 GO:1990169 stress response to copper ion(GO:1990169)
0.3 1.7 GO:0018105 peptidyl-serine phosphorylation(GO:0018105)
0.3 1.0 GO:0048583 regulation of response to stimulus(GO:0048583)
0.3 0.9 GO:0019324 L-lyxose metabolic process(GO:0019324)
0.3 0.9 GO:0015827 tryptophan transport(GO:0015827)
0.2 1.3 GO:0097428 protein maturation by iron-sulfur cluster transfer(GO:0097428)
0.1 0.7 GO:1901661 ubiquinone metabolic process(GO:0006743) ubiquinone biosynthetic process(GO:0006744) ketone biosynthetic process(GO:0042181) quinone metabolic process(GO:1901661) quinone biosynthetic process(GO:1901663)
0.1 2.9 GO:0006970 response to osmotic stress(GO:0006970)
0.1 2.8 GO:0042594 response to starvation(GO:0042594)
0.1 0.8 GO:0006835 dicarboxylic acid transport(GO:0006835) C4-dicarboxylate transport(GO:0015740)
0.1 0.7 GO:0051180 vitamin transport(GO:0051180)
0.1 0.4 GO:0016485 protein processing(GO:0016485)
0.1 0.2 GO:0001121 transcription from bacterial-type RNA polymerase promoter(GO:0001121)
0.0 0.1 GO:0046459 short-chain fatty acid metabolic process(GO:0046459)
0.0 0.2 GO:0042245 RNA repair(GO:0042245)
0.0 0.8 GO:0006766 vitamin metabolic process(GO:0006766) water-soluble vitamin metabolic process(GO:0006767)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.7 2.0 GO:0031235 intrinsic component of the cytoplasmic side of the plasma membrane(GO:0031235)
0.6 4.5 GO:0045203 integral component of cell outer membrane(GO:0045203)
0.2 1.7 GO:0042995 cell projection(GO:0042995)
0.2 0.5 GO:0031237 intrinsic component of periplasmic side of plasma membrane(GO:0031237)
0.1 1.7 GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing(GO:0055052)
0.0 16.8 GO:0005886 plasma membrane(GO:0005886)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
2.4 9.5 GO:0043879 glycolate transmembrane transporter activity(GO:0043879)
1.8 1.8 GO:0003988 acetyl-CoA C-acyltransferase activity(GO:0003988)
1.4 4.3 GO:0003984 acetolactate synthase activity(GO:0003984)
1.0 3.1 GO:0004497 monooxygenase activity(GO:0004497)
0.9 2.6 GO:0046912 AMP binding(GO:0016208) transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer(GO:0046912)
0.8 3.9 GO:0004300 enoyl-CoA hydratase activity(GO:0004300)
0.6 1.7 GO:0008742 L-ribulose-phosphate 4-epimerase activity(GO:0008742)
0.5 1.6 GO:0015113 nitrite transmembrane transporter activity(GO:0015113)
0.5 2.0 GO:0008940 nitrate reductase activity(GO:0008940) metallochaperone activity(GO:0016530)
0.5 2.5 GO:0042301 phosphate ion binding(GO:0042301)
0.4 1.7 GO:0044183 protein binding involved in protein folding(GO:0044183)
0.4 1.1 GO:0015166 polyol transmembrane transporter activity(GO:0015166)
0.3 0.9 GO:0015196 L-tryptophan transmembrane transporter activity(GO:0015196)
0.2 3.8 GO:0008483 transaminase activity(GO:0008483)
0.2 1.3 GO:0008047 enzyme activator activity(GO:0008047)
0.2 0.7 GO:0004659 prenyltransferase activity(GO:0004659)
0.2 1.0 GO:0000156 phosphorelay response regulator activity(GO:0000156)
0.1 1.7 GO:0030170 pyridoxal phosphate binding(GO:0030170)
0.1 0.8 GO:0052689 carboxylic ester hydrolase activity(GO:0052689)
0.1 1.7 GO:0004672 protein kinase activity(GO:0004672)
0.1 0.4 GO:0016151 nickel cation binding(GO:0016151)
0.0 1.8 GO:0005506 iron ion binding(GO:0005506)
0.0 0.2 GO:0000996 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)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 4.0 REACTOME METABOLISM OF CARBOHYDRATES Genes involved in Metabolism of carbohydrates