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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for H-NS

Z-value: 1.56

Transcription factors associated with H-NS

Gene Symbol Gene ID Gene Info
hns
hns DNA-binding transcriptional dual regulator H-NS

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
hns-0.098.2e-01Click!

Activity profile of H-NS motif

Sorted Z-values of H-NS motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
cydAB 4.63
cydA
cydB
cytochrome bd-I terminal oxidase subunit I
cytochrome bd-I terminal oxidase subunit II
gspAB 3.97
gspB
gspA
calcium-binding protein required for initiation of chromosome replication
general secretory pathway component, cryptic
gspCDEFGHIJKLMO 3.27
gspC
gspF
gspG
gspD
gspE
gspJ
gspK
gspH
gspI
gspO
gspL
gspM
putative protein secretion protein for export
putative protein secretion protein for export
putative protein secretion protein for export
putative protein secretion protein for export
putative protein secretion protein for export
putative protein secretion protein for export
putative protein secretion protein for export
putative protein secretion protein for export
putative protein secretion protein for export
leader peptidase, integral membrane protein
putative protein secretion protein for export
putative protein secretion protein
caiF 2.70
caiF
CaiF transcriptional activator
acrEF 2.65
acrF
acrE
AcrEF-TolC multidrug efflux pump - permease subunit
AcrEF-TolC multidrug efflux pump - membrane fusion protein
chiA 2.52
chiA
endochitinase
ydeO 2.30
ydeO
YdeO DNA-binding transcriptional dual regulator
yjjQ-bglJ 1.88
bglJ
yjjQ
BglJ DNA-binding transcriptional regulator
YjjQ DNA-binding transcriptional repressor
proVWX 1.74
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
stpA 1.65
stpA
H-NS-like DNA-binding transcriptional repressor with RNA chaperone activity
hlyE 1.34
hlyE
hemolysin E
yjjP 1.33
yjjP
predicted inner membrane structural protein
fimE 1.21
fimE
regulator for fimA
lacZYA 1.21
lacA
lacY
lacZ
galactoside O-acetyltransferase
lactose / melibiose:H+ symporter LacY
β-galactosidase
bglGFB 1.14
bglB
bglG
bglF
6-phospho-β-glucosidase B; cryptic
BglG transcriptional antiterminator
BglF
ilvIH 1.07
ilvI
ilvH
acetolactate synthase / acetohydroxybutanoate synthase, catalytic subunit
acetolactate synthase / acetohydroxybutanoate synthase, regulatory subunit
gadXW 1.06
gadW
gadX
GadW DNA-binding transcriptional dual regulator
GadX DNA-binding transcriptional dual regulator
gadX 1.02
gadX
GadX DNA-binding transcriptional dual regulator
caiTABCDE 0.96
caiT
caiE
caiD
caiC
caiB
caiA
L-carnitine : γ-butyrobetaine antiporter
predicted acyl transferase
crotonobetainyl-CoA hydratase
carnitine-CoA ligase
γ-butyrobetainyl-CoA:carnitine CoA transferase
crotonobetainyl-CoA reductase
rcsA 0.96
rcsA
positive DNA-binding transcriptional regulator of capsular polysaccharide synthesis, activates its own expression
hdfR 0.93
hdfR
HdfR DNA-binding transcriptional dual regulator
cadC 0.78
cadC
CadC DNA-binding transcriptional activator
srlAEBD-gutM-srlR-gutQ 0.78
srlB
srlA
srlE
srlD
gutQ
srlR
gutM
sorbitol PTS permease - SrlB subunit
sorbitol PTS permease - SrlA subunit
sorbitol PTS permease - SrlE subunit
sorbitol-6-phosphate dehydrogenase
D-arabinose 5-phosphate isomerase
GutR DNA-binding transcriptional repressor
GutM DNA-binding transcriptional activator
micF 0.71
micF
MicF
yciGFE 0.69
yciG
yciF
yciE
predicted protein
conserved protein
conserved protein
casABCDE12 0.69
casE
casD
casA
casC
casB
cas1
cas2
crRNA endonuclease
Cascade subunit D
Cascade subunit A
Cascade subunit C
Cascade subunit B
multifunctional nuclease Cas1
Cas2 protein
hns 0.65
hns
H-NS DNA-binding transcriptional dual regulator
rrsH-ileV-alaV-rrlH-rrfH 0.64
rrlH
rrfH
rrsH
ileV
alaV
rrlH 23S ribosomal RNA
rrfH 5S ribosomal RNA
rrsH 16S ribosomal RNA
tRNAileV
tRNAalaV
rrsB-gltT-rrlB-rrfB 0.62
rrlB
gltT
rrfB
rrsB
rrlB 23S ribosomal RNA
tRNAgltT
rrfB 5S ribosomal RNA
rrsB 16S ribosomal RNA
ssrS 0.58
ssrS
6S RNA
csiD-lhgO-gabDTP 0.57
gabD
lhgO
gabP
csiD
gabT
succinate-semialdehyde dehydrogenase (NADP+)
L-2-hydroxyglutarate oxidase
4-aminobutyrate:H+ symporter
predicted protein
4-aminobutyrate aminotransferase
fes-ybdZ-entF-fepE 0.50
ybdZ
fes
fepE
entF
MbtH-like protein that enhances the catalytic function of EntF
enterochelin esterase
ferric enterobactin (enterochelin) transport
apo-serine activating enzyme
rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF 0.44
rrlD
ileU
alaU
thrV
rrfF
rrsD
rrfD
rrlD 23S ribosomal RNA
tRNAileU
tRNAalaU
tRNAthrV
rrfF 5S ribosomal RNA
rrsD 16S ribosomal RNA
rrfD 5S ribosomal RNA
gadW 0.42
gadW
GadW DNA-binding transcriptional dual regulator
gadAX 0.39
gadX
gadA
GadX DNA-binding transcriptional dual regulator
glutamate decarboxylase A subunit
hdeD 0.39
hdeD
acid-resistance membrane protein
cadBA 0.38
cadA
cadB
lysine decarboxylase 1
lysine:cadaverine antiporter
cysPUWAM 0.37
cysU
cysM
cysW
cysA
cysP
sulfate / thiosulfate ABC transporter - membrane subunit
cysteine synthase B
sulfate / thiosulfate ABC transporter - membrane subunit
sulfate / thiosulfate ABC transporter - ATP binding subunit
sulfate / thiosulfate ABC transporter - periplasmic binding protein CysP
fliC 0.37
fliC
flagellar biosynthesis; flagellin, filament structural protein
rrsG-gltW-rrlG-rrfG 0.35
rrlG
gltW
rrfG
rrsG
rrlG 23S ribosomal RNA
tRNAgltW
rrfG 5S ribosomal RNA
rrsG 16S ribosomal RNA
rrsC-gltU-rrlC-rrfC 0.29
rrlC
gltU
rrfC
rrsC
rrlC 23S ribosomal RNA
tRNAgltU
rrfC 5S ribosomal RNA
rrsC 16S ribosomal RNA
yhiM 0.27
yhiM
inner membrane protein with a role in acid resistance
slp-dctR 0.18
slp
dctR
starvation lipoprotein
predicted DNA-binding transcriptional regulator
adiA 0.17
adiA
arginine decarboxylase, degradative
garPLRK-rnpB 0.13
garL
rnpB
garR
garK
garP
α-dehydro-β-deoxy-D-glucarate aldolase
RnpB
tartronate semialdehyde reductase
glycerate kinase I
galactarate / glucarate / glycerate transporter GarP
fimAICDFGH 0.12
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
adeD 0.09
adeD
cryptic adenine deaminase
galETKM 0.03
galT
galE
galM
galK
galactose-1-phosphate uridylyltransferase
UDP-glucose 4-epimerase
galactose-1-epimerase
galactokinase
nirBDC-cysG 0.01
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 H-NS

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
1.2 3.7 GO:0009437 carnitine metabolic process(GO:0009437)
1.2 4.6 GO:0019646 aerobic electron transport chain(GO:0019646)
0.9 1.7 GO:0015697 quaternary ammonium group transport(GO:0015697) amino-acid betaine transport(GO:0015838)
0.4 1.3 GO:0051715 cell killing(GO:0001906) cytolysis(GO:0019835) killing of cells of other organism(GO:0031640) modification of morphology or physiology of other organism(GO:0035821) disruption of cells of other organism(GO:0044364) cytolysis in other organism(GO:0051715)
0.4 3.3 GO:0071806 protein transmembrane transport(GO:0071806)
0.3 1.1 GO:0009097 isoleucine metabolic process(GO:0006549) isoleucine biosynthetic process(GO:0009097)
0.3 0.8 GO:0006059 hexitol metabolic process(GO:0006059) hexitol catabolic process(GO:0019407)
0.2 0.7 GO:0090502 maintenance of DNA repeat elements(GO:0043570) maintenance of CRISPR repeat elements(GO:0043571) RNA phosphodiester bond hydrolysis, endonucleolytic(GO:0090502)
0.2 1.6 GO:0006855 drug transmembrane transport(GO:0006855)
0.2 0.7 GO:0051595 response to methylglyoxal(GO:0051595) response to ketone(GO:1901654)
0.2 0.5 GO:0019290 siderophore metabolic process(GO:0009237) enterobactin metabolic process(GO:0009238) enterobactin biosynthetic process(GO:0009239) catechol-containing compound metabolic process(GO:0009712) catechol-containing compound biosynthetic process(GO:0009713) nonribosomal peptide biosynthetic process(GO:0019184) siderophore biosynthetic process(GO:0019290) siderophore biosynthetic process from catechol(GO:0019540) phenol-containing compound biosynthetic process(GO:0046189)
0.2 1.2 GO:0015766 disaccharide transport(GO:0015766) disaccharide catabolic process(GO:0046352)
0.1 0.6 GO:0051454 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)
0.1 0.4 GO:0006535 cysteine biosynthetic process from serine(GO:0006535)
0.1 0.6 GO:0042450 ornithine metabolic process(GO:0006591) arginine biosynthetic process via ornithine(GO:0042450)
0.1 0.6 GO:0071978 bacterial-type flagellum-dependent swarming motility(GO:0071978)
0.1 0.4 GO:0015695 organic cation transport(GO:0015695)
0.1 1.1 GO:0034219 carbohydrate transmembrane transport(GO:0034219)
0.1 0.2 GO:0031329 regulation of cellular catabolic process(GO:0031329) regulation of cellular carbohydrate catabolic process(GO:0043471)
0.1 0.3 GO:0071229 cellular response to acid chemical(GO:0071229)
0.0 0.1 GO:0015074 DNA integration(GO:0015074)
0.0 0.1 GO:0019577 aldaric acid metabolic process(GO:0019577) aldaric acid catabolic process(GO:0019579)
0.0 0.1 GO:0009297 pilus assembly(GO:0009297)
0.0 2.2 GO:0051254 positive regulation of transcription, DNA-templated(GO:0045893) positive regulation of RNA metabolic process(GO:0051254) positive regulation of RNA biosynthetic process(GO:1902680) positive regulation of nucleic acid-templated transcription(GO:1903508)
0.0 0.1 GO:0046100 purine nucleobase catabolic process(GO:0006145) purine nucleobase biosynthetic process(GO:0009113) hypoxanthine metabolic process(GO:0046100)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.5 4.6 GO:0070069 cytochrome complex(GO:0070069)
0.3 1.3 GO:0005576 extracellular region(GO:0005576)
0.3 1.2 GO:0043227 membrane-bounded organelle(GO:0043227) intracellular membrane-bounded organelle(GO:0043231)
0.1 1.1 GO:1990234 transferase complex(GO:1990234)
0.0 11.4 GO:0031226 intrinsic component of plasma membrane(GO:0031226)
0.0 4.8 GO:0005886 plasma membrane(GO:0005886)
0.0 0.1 GO:0042995 cell projection(GO:0042995)
0.0 1.0 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.5 4.6 GO:0016679 oxidoreductase activity, acting on diphenols and related substances as donors(GO:0016679) oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor(GO:0016682)
0.6 1.7 GO:0099600 amine transmembrane transporter activity(GO:0005275) transmembrane receptor activity(GO:0099600)
0.5 1.0 GO:0015199 amino-acid betaine transmembrane transporter activity(GO:0015199) quaternary ammonium group transmembrane transporter activity(GO:0015651)
0.4 1.2 GO:0070492 O-acetyltransferase activity(GO:0016413) oligosaccharide binding(GO:0070492)
0.4 0.4 GO:0015491 cation:cation antiporter activity(GO:0015491)
0.4 1.1 GO:0008706 6-phospho-beta-glucosidase activity(GO:0008706)
0.4 1.1 GO:0003984 acetolactate synthase activity(GO:0003984)
0.3 0.8 GO:0019146 arabinose-5-phosphate isomerase activity(GO:0019146)
0.3 0.5 GO:0015620 ferric-enterobactin transmembrane transporter activity(GO:0015620)
0.2 1.8 GO:0001140 transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding(GO:0001140)
0.2 0.6 GO:0004777 succinate-semialdehyde dehydrogenase (NAD+) activity(GO:0004777)
0.2 2.5 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds(GO:0004553)
0.1 0.7 GO:0016889 crossover junction endodeoxyribonuclease activity(GO:0008821) endodeoxyribonuclease activity, producing 3'-phosphomonoesters(GO:0016889)
0.1 1.3 GO:0015238 drug transmembrane transporter activity(GO:0015238)
0.1 0.6 GO:0003681 bent DNA binding(GO:0003681)
0.1 6.0 GO:0003700 transcription factor activity, sequence-specific DNA binding(GO:0003700)
0.1 0.4 GO:0080146 L-cysteine desulfhydrase activity(GO:0080146)
0.1 2.3 GO:0008233 peptidase activity(GO:0008233)
0.0 0.1 GO:0048029 monosaccharide binding(GO:0048029)
0.0 0.1 GO:0004096 catalase activity(GO:0004096)
0.0 0.1 GO:0016662 oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor(GO:0016662)