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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for IHF

Z-value: 0.50

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-0.811.5e-02Click!
infB-0.772.6e-02Click!

Activity profile of IHF motif

Sorted Z-values of IHF motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
yadV-htrE 2.86
htrE
yadV
putative outer membrane usher protein
probable pilin chaperone similar to PapD
acs-yjcH-actP 1.95
acs
actP
yjcH
acetyl-CoA synthetase (AMP-forming)
acetate / glycolate : cation symporter
conserved inner membrane protein
dcuD 0.81
dcuD
putative transport protein, C4-dicarboxylate uptake C family
ilvLXG_1G_2MEDA 0.77
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
gcd 0.70
gcd
quinoprotein glucose dehydrogenase
yeiL 0.64
yeiL
YeiL DNA-binding transcriptional activator
hycABCDEFGHI 0.62
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
sufABCDSE 0.61
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
ssuEADCB 0.61
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
yiaKLMNO-lyxK-sgbHUE 0.59
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
dppABCDF 0.59
dppA
dppB
dppC
dppD
dppF
dipeptide ABC transporter - periplasmic binding protein
dipeptide ABC transporter - predicted membrane subunit
dipeptide ABC transporter - predicted membrane subunit
dipeptide ABC transporter - predicted ATP binding subunit
dipeptide ABC transporter - predicted ATP binding subunit
tyrP 0.50
tyrP
tyrosine:H+ symporter TyrP
carAB 0.48
carB
carA
carbamoyl phosphate synthetase, β chain
carbamoyl phosphate synthetase, α chain
yjbEFGH 0.46
yjbG
yjbF
yjbE
yjbH
conserved protein
predicted lipoprotein
predicted protein
predicted porin
rtcBA 0.44
rtcB
rtcA
RNA-splicing ligase RtcB
RNA 3'-terminal phosphate cyclase
patA 0.42
patA
putrescine aminotransferase
osmE 0.42
osmE
osmotically inducible protein OsmE
atoDAEB 0.40
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
glcDEFGBA 0.38
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
proVWX 0.37
proX
proW
proV
glycine betaine / proline ABC transporter - periplasmic binding protein
glycine betaine / proline ABC transporter - membrane subunit
glycine betaine / proline ABC transporter - ATP binding subunit
gltA 0.36
gltA
citrate synthase
osmY 0.34
osmY
periplasmic chaperone, osmotically induced
ubiCA 0.32
ubiC
ubiA
chorismate lyase
4-hydroxybenzoate octaprenyltransferase
hipBA 0.31
hipA
hipB
serine/threonine kinase HipA
HipB antitoxin and DNA-binding transcriptional repressor
ulaG 0.29
ulaG
L-ascorbate 6-phosphate lactonase
mtr 0.29
mtr
tryptohan / indole:H+ symporter Mtr
nirBDC-cysG 0.29
nirD
cysG
nirC
nirB
nitrite reductase, small subunit
siroheme synthase subunit
nitrite transporter NirC
nitrite reductase, large subunit
glpTQ 0.29
glpT
glpQ
glycerol-3-phosphate:phosphate antiporter
glycerophosphoryl diester phosphodiesterase, periplasmic
paaZ 0.27
paaZ
oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase
ulaABCDEF 0.26
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
yjbE 0.26
yjbE
predicted protein
csgDEFG 0.25
csgG
csgF
csgE
csgD
curli secretion channel
curli assembly component
curli transport specificity factor
CsgD DNA-binding transcriptional dual regulator
pstSCA 0.23
pstS
pstC
pstA
phosphate ABC transporter - periplasmic binding protein
phosphate ABC transporter - membrane subunit
phosphate ABC transporter - membrane subunit
pspG 0.20
pspG
phage shock protein G
pstSCAB-phoU 0.18
pstS
pstC
pstA
phoU
pstB
phosphate ABC transporter - periplasmic binding protein
phosphate ABC transporter - membrane subunit
phosphate ABC transporter - membrane subunit
negative regulator of the pho regulon
phosphate ABC transporter - ATP binding subunit
rpoH 0.18
rpoH
RNA polymerase, sigma 32 (sigma H) factor
paaABCDEFGHIJK 0.16
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
ompR-envZ 0.13
envZ
ompR
EnvZ
OmpR transcriptional dual regulator
norVW 0.12
norW
norV
NADH:flavorubredoxin reductase
flavorubredoxin
adiA 0.12
adiA
arginine decarboxylase, degradative
pstS 0.11
pstS
phosphate ABC transporter - periplasmic binding protein
aceBAK 0.09
aceK
aceB
aceA
isocitrate dehydrogenase phosphatase / isocitrate dehydrogenase kinase
malate synthase A
isocitrate lyase
fimAICDFGH 0.09
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
nrfABCDEFG 0.06
nrfF
nrfG
nrfD
nrfE
nrfB
nrfC
nrfA
activator of formate-dependent nitrite reductase complex
NrfG
formate dependent nitrite reductase - NrfD subunit
formate-dependent nitrite reductase; possible assembly function
formate-dependent nitrite reductase - penta-heme cytochrome c
formate-dependent nitrite reductase, 4Fe-4S subunit
formate dependent nitrite reductase - NrfA subunit
hemF 0.04
hemF
coproporphyrinogen III oxidase
narGHJI 0.03
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

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
0.7 3.0 GO:0043711 pilus organization(GO:0043711)
0.7 2.0 GO:0018394 tellurite transport(GO:0015710) peptidyl-lysine acetylation(GO:0018394) post-translational protein modification(GO:0043687)
0.2 0.7 GO:0045226 extracellular polysaccharide biosynthetic process(GO:0045226) extracellular polysaccharide metabolic process(GO:0046379)
0.2 0.7 GO:0006007 glucose catabolic process(GO:0006007)
0.2 0.6 GO:0042908 cellular response to sulfate starvation(GO:0009970) xenobiotic transport(GO:0042908)
0.2 0.6 GO:0019324 L-lyxose metabolic process(GO:0019324)
0.2 0.6 GO:0015886 heme transport(GO:0015886)
0.2 0.8 GO:0006549 isoleucine metabolic process(GO:0006549) isoleucine biosynthetic process(GO:0009097)
0.1 0.4 GO:0010124 phenylacetate catabolic process(GO:0010124)
0.1 0.4 GO:0019626 short-chain fatty acid catabolic process(GO:0019626)
0.1 0.4 GO:0015838 quaternary ammonium group transport(GO:0015697) amino-acid betaine transport(GO:0015838)
0.1 0.6 GO:0016485 protein processing(GO:0016485)
0.1 0.5 GO:0046487 glyoxylate metabolic process(GO:0046487)
0.1 0.8 GO:0015740 C4-dicarboxylate transport(GO:0015740)
0.1 0.4 GO:0042245 RNA repair(GO:0042245)
0.1 0.5 GO:0010921 regulation of phosphatase activity(GO:0010921)
0.1 0.6 GO:0097428 protein maturation by iron-sulfur cluster transfer(GO:0097428)
0.1 0.3 GO:0015827 tryptophan transport(GO:0015827)
0.1 0.5 GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process(GO:0006207) pyrimidine nucleobase biosynthetic process(GO:0019856)
0.1 0.3 GO:0022611 dormancy process(GO:0022611)
0.1 0.3 GO:0015791 polyol transport(GO:0015791)
0.1 0.4 GO:0009447 polyamine catabolic process(GO:0006598) putrescine catabolic process(GO:0009447)
0.1 0.3 GO:0042181 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 0.1 GO:0017006 protein-heme linkage(GO:0017003) protein-tetrapyrrole linkage(GO:0017006) cytochrome c-heme linkage(GO:0018063)
0.1 1.2 GO:0006970 response to osmotic stress(GO:0006970)
0.0 0.2 GO:1900190 regulation of multi-organism process(GO:0043900) regulation of single-species biofilm formation(GO:1900190)
0.0 0.1 GO:0046209 nitric oxide metabolic process(GO:0046209) nitric oxide catabolic process(GO:0046210) cellular response to nitrogen compound(GO:1901699) cellular response to reactive nitrogen species(GO:1902170)
0.0 0.1 GO:0006527 arginine catabolic process(GO:0006527)
0.0 0.3 GO:0051180 vitamin transport(GO:0051180)
0.0 0.2 GO:0001121 transcription from bacterial-type RNA polymerase promoter(GO:0001121)
0.0 0.0 GO:2001057 reactive nitrogen species metabolic process(GO:2001057)
0.0 0.3 GO:0046365 monosaccharide catabolic process(GO:0046365)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 1.2 GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing(GO:0055052)
0.0 0.2 GO:0031246 intrinsic component of periplasmic side of cell outer membrane(GO:0031246)
0.0 0.1 GO:0045203 integral component of cell outer membrane(GO:0045203)
0.0 4.1 GO:0005887 integral component of plasma membrane(GO:0005887)
0.0 0.1 GO:0042995 cell projection(GO:0042995)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.7 2.0 GO:0015118 tellurite transmembrane transporter activity(GO:0015118) tellurite uptake transmembrane transporter activity(GO:0015654)
0.3 0.9 GO:0008742 L-ribulose-phosphate 4-epimerase activity(GO:0008742)
0.3 0.8 GO:0003984 acetolactate synthase activity(GO:0003984)
0.2 0.7 GO:0016901 oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor(GO:0016901)
0.2 0.6 GO:0004497 monooxygenase activity(GO:0004497)
0.2 0.6 GO:0015198 oligopeptide transporter activity(GO:0015198) oligopeptide transmembrane transporter activity(GO:0035673)
0.2 0.4 GO:0043879 glycolate transmembrane transporter activity(GO:0043879)
0.1 0.4 GO:0008410 CoA-transferase activity(GO:0008410)
0.1 0.4 GO:0005275 amine transmembrane transporter activity(GO:0005275) transmembrane receptor activity(GO:0099600)
0.1 0.5 GO:0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor(GO:0016884)
0.1 0.7 GO:0015114 phosphate ion transmembrane transporter activity(GO:0015114)
0.1 0.3 GO:0001047 core promoter binding(GO:0001047)
0.1 0.3 GO:0015196 L-tryptophan transmembrane transporter activity(GO:0015196)
0.1 0.3 GO:0004325 ferrochelatase activity(GO:0004325)
0.1 0.3 GO:0016803 hydrolase activity, acting on ether bonds(GO:0016801) ether hydrolase activity(GO:0016803)
0.1 0.6 GO:0008047 enzyme activator activity(GO:0008047)
0.1 0.3 GO:0004659 prenyltransferase activity(GO:0004659)
0.1 0.2 GO:0016289 3-hydroxyacyl-CoA dehydrogenase activity(GO:0003857) CoA hydrolase activity(GO:0016289) thiolester hydrolase activity(GO:0016790)
0.0 0.1 GO:0042301 phosphate ion binding(GO:0042301)
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)
0.0 0.1 GO:0046912 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer(GO:0046912)
0.0 0.3 GO:0052689 carboxylic ester hydrolase activity(GO:0052689)
0.0 0.6 GO:0004175 endopeptidase activity(GO:0004175)
0.0 0.4 GO:0008483 transaminase activity(GO:0008483)
0.0 0.1 GO:0000156 phosphorelay response regulator activity(GO:0000156)
0.0 0.1 GO:0044183 protein binding involved in protein folding(GO:0044183)
0.0 0.2 GO:0016661 oxidoreductase activity, acting on other nitrogenous compounds as donors(GO:0016661)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.4 REACTOME METABOLISM OF CARBOHYDRATES Genes involved in Metabolism of carbohydrates