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GSE80451: E.coli grown aerobically and anaerobically

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Results for IHF

Z-value: 1.12

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
infB0.951.3e-02Click!
infA-0.029.8e-01Click!

Activity profile of IHF motif

Sorted Z-values of IHF motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
osmY 3.20
osmY
periplasmic chaperone, osmotically induced
ompC 2.70
ompC
outer membrane protein C
sodA 2.30
sodA
superoxide dismutase (Mn)
narK 2.29
narK
nitrate:nitrite antiporter NarK
ihfA 2.09
ihfA
integration host factor (IHF), α subunit
osmE 1.94
osmE
osmotically inducible protein OsmE
uspB 1.90
uspB
predicted universal stress (ethanol tolerance) protein B
dps 1.78
dps
stationary phase nucleoid protein that sequesters iron and protects DNA from damage
mtr 1.76
mtr
tryptohan / indole:H+ symporter Mtr
sufABCDSE 1.67
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
fnr 1.39
fnr
FNR DNA-binding transcriptional dual regulator
gcd 1.32
gcd
quinoprotein glucose dehydrogenase
narGHJI 1.31
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 1.29
yjbE
predicted protein
pspG 1.27
pspG
phage shock protein G
ndh 1.19
ndh
NADH:quinone oxidoreductase II
folA 1.19
folA
dihydrofolate reductase
patA 1.11
patA
putrescine aminotransferase
rtcBA 0.89
rtcB
rtcA
RNA-splicing ligase RtcB
RNA 3'-terminal phosphate cyclase
focA-pflB 0.86
focA
pflB
formate channel FocA
pyruvate formate-lyase (inactive)
glmY 0.79
glmY
GlmY
yjbEFGH 0.78
yjbG
yjbF
yjbE
yjbH
conserved protein
predicted lipoprotein
predicted protein
predicted porin
glcDEFGBA 0.72
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
fimAICDFGH 0.62
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
hycABCDEFGHI 0.52
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
hipBA 0.49
hipA
hipB
serine/threonine kinase HipA
HipB antitoxin and DNA-binding transcriptional repressor
ulaG 0.46
ulaG
L-ascorbate 6-phosphate lactonase
nuoABCEFGHIJKLMN 0.46
nuoB
nuoC
nuoA
nuoF
nuoG
nuoE
nuoJ
nuoK
nuoH
nuoI
nuoN
nuoL
nuoM
NADH:ubiquinone oxidoreductase, chain B
NADH:ubiquinone oxidoreductase, chain CD
NADH:ubiquinone oxidoreductase, membrane subunit A
NADH:ubiquinone oxidoreductase, chain F
NADH:ubiquinone oxidoreductase, chain G
NADH:ubiquinone oxidoreductase, chain E
NADH:ubiquinone oxidoreductase, membrane subunit J
NADH:ubiquinone oxidoreductase, membrane subunit K
NADH:ubiquinone oxidoreductase, membrane subunit H
NADH:ubiquinone oxidoreductase, chain I
NADH:ubiquinone oxidoreductase, membrane subunit N
NADH:ubiquinone oxidoreductase, membrane subunit L
NADH:ubiquinone oxidoreductase, membrane subunit M
acs-yjcH-actP 0.38
acs
actP
yjcH
acetyl-CoA synthetase (AMP-forming)
acetate / glycolate : cation symporter
conserved inner membrane protein
ompR-envZ 0.34
envZ
ompR
EnvZ
OmpR transcriptional dual regulator
cysJIH 0.33
cysI
cysH
cysJ
sulfite reductase, hemoprotein subunit
3'-phospho-adenylylsulfate reductase
sulfite reductase, flavoprotein subunit
ibpB 0.28
ibpB
small heat shock protein IbpB
hypABCDE-fhlA 0.28
fhlA
hypE
hypD
hypA
hypC
hypB
FhlA transcriptional activator
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
glnHPQ 0.27
glnH
glnQ
glnP
L-glutamine ABC transporter - periplasmic binding protein
L-glutamine ABC transporter - ATP binding subunit
L-glutamine ABC transporter - membrane subunit
dusB-fis 0.26
fis
dusB
Fis DNA-binding transcriptional dual regulator
tRNA-dihydrouridine synthase B
amiA-hemF 0.21
hemF
amiA
coproporphyrinogen III oxidase
N-acetylmuramoyl-L-alanine amidase A
hypABCDE 0.20
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
dmsABC 0.19
dmsA
dmsB
dmsC
dimethyl sulfoxide reductase, chain A
dimethyl sulfoxide reductase, chain B
dimethyl sulfoxide reductase, chain C
sodB 0.19
sodB
superoxide dismutase (Fe)
uspA 0.08
uspA
universal stress global stress response regulator
ulaABCDEF 0.07
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
nirBDC-cysG 0.00
nirD
cysG
nirC
nirB
nitrite reductase, small subunit
siroheme synthase subunit
nitrite transporter NirC
nitrite reductase, large subunit

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
0.8 2.5 GO:0006801 response to superoxide(GO:0000303) superoxide metabolic process(GO:0006801)
0.8 2.3 GO:0015707 nitrite transport(GO:0015707)
0.7 2.1 GO:0046379 extracellular polysaccharide biosynthetic process(GO:0045226) extracellular polysaccharide metabolic process(GO:0046379)
0.6 1.9 GO:0097305 response to alcohol(GO:0097305)
0.6 1.8 GO:0015827 tryptophan transport(GO:0015827)
0.4 1.3 GO:0006007 glucose catabolic process(GO:0006007)
0.4 1.3 GO:0071941 nitrogen cycle metabolic process(GO:0071941)
0.4 1.2 GO:0043207 response to biotic stimulus(GO:0009607) response to virus(GO:0009615) response to external biotic stimulus(GO:0043207) response to other organism(GO:0051707)
0.3 3.1 GO:0006972 hyperosmotic response(GO:0006972)
0.3 1.3 GO:0015748 organophosphate ester transport(GO:0015748)
0.3 1.2 GO:0019646 aerobic electron transport chain(GO:0019646)
0.3 1.7 GO:0097428 protein maturation by iron-sulfur cluster transfer(GO:0097428)
0.2 1.2 GO:0046654 tetrahydrofolate biosynthetic process(GO:0046654)
0.2 0.9 GO:0042245 RNA repair(GO:0042245)
0.2 0.6 GO:0009297 pilus assembly(GO:0009297)
0.2 2.3 GO:0006970 response to osmotic stress(GO:0006970)
0.2 0.4 GO:0043687 post-translational protein modification(GO:0043687)
0.2 1.1 GO:0009447 polyamine catabolic process(GO:0006598) putrescine catabolic process(GO:0009447)
0.2 0.5 GO:1902600 hydrogen ion transmembrane transport(GO:1902600)
0.1 0.7 GO:0034308 primary alcohol metabolic process(GO:0034308)
0.1 0.5 GO:0018249 protein dehydration(GO:0018249) peptidyl-S-carbamoyl-L-cysteine dehydration(GO:0046892)
0.1 0.5 GO:0016485 protein processing(GO:0016485)
0.1 0.5 GO:0036289 dormancy process(GO:0022611) peptidyl-serine autophosphorylation(GO:0036289)
0.1 1.2 GO:0009061 anaerobic respiration(GO:0009061)
0.1 0.9 GO:0015718 monocarboxylic acid transport(GO:0015718)
0.1 0.3 GO:1990169 stress response to copper ion(GO:1990169)
0.1 0.2 GO:0097237 cellular response to antibiotic(GO:0071236) cellular response to toxic substance(GO:0097237)
0.0 1.3 GO:0042594 response to starvation(GO:0042594)
0.0 0.3 GO:0051276 chromosome organization(GO:0051276)
0.0 0.5 GO:0006767 water-soluble vitamin metabolic process(GO:0006767)
0.0 0.3 GO:0006790 sulfur compound metabolic process(GO:0006790)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 1.3 GO:0031235 intrinsic component of the cytoplasmic side of the plasma membrane(GO:0031235)
0.4 3.5 GO:0045203 integral component of cell outer membrane(GO:0045203)
0.2 0.6 GO:0042995 cell projection(GO:0042995)
0.1 0.5 GO:0098803 respiratory chain(GO:0070469) plasma membrane respiratory chain(GO:0070470) respiratory chain complex(GO:0098803)
0.1 0.2 GO:0031237 intrinsic component of periplasmic side of plasma membrane(GO:0031237)
0.1 0.3 GO:0044427 chromosome(GO:0005694) chromosomal part(GO:0044427)
0.0 0.4 GO:0031234 extrinsic component of cytoplasmic side of plasma membrane(GO:0031234)
0.0 0.3 GO:0009898 cytoplasmic side of plasma membrane(GO:0009898) cytoplasmic side of membrane(GO:0098562)
0.0 1.4 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)
0.0 4.2 GO:0005887 integral component of plasma membrane(GO:0005887)
0.0 2.4 GO:0005886 plasma membrane(GO:0005886)
0.0 1.4 GO:0016020 membrane(GO:0016020)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.8 2.5 GO:0016721 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
0.8 2.3 GO:0015113 nitrite transmembrane transporter activity(GO:0015113)
0.6 1.8 GO:0015196 L-tryptophan transmembrane transporter activity(GO:0015196)
0.5 1.6 GO:0008137 NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
0.4 1.3 GO:0048039 oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor(GO:0016901) ubiquinone binding(GO:0048039)
0.3 1.3 GO:0008940 nitrate reductase activity(GO:0008940) metallochaperone activity(GO:0016530)
0.3 1.6 GO:0016783 sulfurtransferase activity(GO:0016783)
0.3 1.1 GO:0043879 glycolate transmembrane transporter activity(GO:0043879)
0.2 1.4 GO:0016646 oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor(GO:0016646)
0.2 0.6 GO:0044183 protein binding involved in protein folding(GO:0044183)
0.1 0.5 GO:0070025 carbon monoxide binding(GO:0070025)
0.1 0.9 GO:0008028 monocarboxylic acid transmembrane transporter activity(GO:0008028)
0.1 0.2 GO:0008745 N-acetylmuramoyl-L-alanine amidase activity(GO:0008745)
0.1 0.5 GO:0016151 nickel cation binding(GO:0016151)
0.1 0.3 GO:0000156 phosphorelay response regulator activity(GO:0000156)
0.0 0.5 GO:0052689 carboxylic ester hydrolase activity(GO:0052689)
0.0 1.2 GO:0005506 iron ion binding(GO:0005506)
0.0 1.1 GO:0003700 transcription factor activity, sequence-specific DNA binding(GO:0003700)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.7 REACTOME METABOLISM OF CARBOHYDRATES Genes involved in Metabolism of carbohydrates