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

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Results for H-NS

Z-value: 3.76

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-0.844.3e-08Click!

Activity profile of H-NS motif

Sorted Z-values of H-NS motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
cydAB 87.20
cydA
cydB
cytochrome bd-I terminal oxidase subunit I
cytochrome bd-I terminal oxidase subunit II
gspAB 42.64
gspB
gspA
calcium-binding protein required for initiation of chromosome replication
general secretory pathway component, cryptic
ssrS 42.28
ssrS
6S RNA
ssrS-fau 42.25
ssrS
fau
6S RNA
5-formyltetrahydrofolate cyclo-ligase
gspCDEFGHIJKLMO 36.78
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
rrsB-gltT-rrlB-rrfB 31.89
rrlB
gltT
rrfB
rrsB
rrlB 23S ribosomal RNA
tRNAgltT
rrfB 5S ribosomal RNA
rrsB 16S ribosomal RNA
rrsC-gltU-rrlC-rrfC 29.38
rrlC
gltU
rrfC
rrsC
rrlC 23S ribosomal RNA
tRNAgltU
rrfC 5S ribosomal RNA
rrsC 16S ribosomal RNA
rrsG-gltW-rrlG-rrfG 28.91
rrlG
gltW
rrfG
rrsG
rrlG 23S ribosomal RNA
tRNAgltW
rrfG 5S ribosomal RNA
rrsG 16S ribosomal RNA
hdeD 27.10
hdeD
acid-resistance membrane protein
cadC 24.82
cadC
CadC DNA-binding transcriptional activator
rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF 23.35
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
rrsH-ileV-alaV-rrlH-rrfH 23.35
rrlH
rrfH
rrsH
ileV
alaV
rrlH 23S ribosomal RNA
rrfH 5S ribosomal RNA
rrsH 16S ribosomal RNA
tRNAileV
tRNAalaV
rcsDB 21.78
rcsB
rcsD
RcsB
RcsD phosphotransferase
ydeO 21.47
ydeO
YdeO DNA-binding transcriptional dual regulator
casABCDE12 21.33
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
fliC 20.41
fliC
flagellar biosynthesis; flagellin, filament structural protein
adiY 19.16
adiY
AdiY DNA-binding transcriptional activator
adiA 18.53
adiA
arginine decarboxylase, degradative
lacZYA 18.34
lacA
lacY
lacZ
galactoside O-acetyltransferase
lactose / melibiose:H+ symporter LacY
β-galactosidase
acrEF 17.87
acrF
acrE
AcrEF-TolC multidrug efflux pump - permease subunit
AcrEF-TolC multidrug efflux pump - membrane fusion protein
fimE 17.81
fimE
regulator for fimA
fimAICDFGH 17.77
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
caiF 16.95
caiF
CaiF transcriptional activator
csiE 16.87
csiE
stationary phase inducible protein
hchA 16.08
hchA
amino acid deglycase Hsp31
proVWX 15.47
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
bolA 14.44
bolA
BolA DNA-binding transcriptional dual regulator
asr 14.21
asr
acid shock protein
caiTABCDE 13.67
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
garPLRK-rnpB 13.40
garL
rnpB
garR
garK
garP
α-dehydro-β-deoxy-D-glucarate aldolase
RnpB
tartronate semialdehyde reductase
glycerate kinase I
galactarate / glucarate / glycerate transporter GarP
adeD 13.33
adeD
cryptic adenine deaminase
hlyE 13.26
hlyE
hemolysin E
yjjP 13.19
yjjP
predicted inner membrane structural protein
yjjQ-bglJ 12.03
bglJ
yjjQ
BglJ DNA-binding transcriptional regulator
YjjQ DNA-binding transcriptional repressor
chiA 11.78
chiA
endochitinase
cadBA 11.59
cadA
cadB
lysine decarboxylase 1
lysine:cadaverine antiporter
yhiM 11.25
yhiM
inner membrane protein with a role in acid resistance
nrdDG 11.18
nrdD
nrdG
anaerobic ribonucleoside-triphosphate reductase
anaerobic ribonucleoside-triphosphate reductase-activating protein
gadX 10.07
gadX
GadX DNA-binding transcriptional dual regulator
cspD 9.61
cspD
DNA replication inhibitor
appY 9.45
appY
AppY DNA-binding transcriptional activator
galE 9.42
galE
UDP-glucose 4-epimerase
gadXW 8.66
gadW
gadX
GadW DNA-binding transcriptional dual regulator
GadX DNA-binding transcriptional dual regulator
yciG 8.64
yciG
predicted protein
gadW 7.90
gadW
GadW DNA-binding transcriptional dual regulator
leuO 7.17
leuO
LeuO DNA-binding transcriptional dual regulator
galET 7.16
galT
galE
galactose-1-phosphate uridylyltransferase
UDP-glucose 4-epimerase
yciGFE 6.86
yciG
yciF
yciE
predicted protein
conserved protein
conserved protein
hdeAB-yhiD 6.18
yhiD
hdeB
hdeA
inner membrane protein YhiD
HdeB monomer
HdeA monomer, chaperone active form
osmC 6.09
osmC
osmotically inducible peroxiredoxin
slp-dctR 5.48
slp
dctR
starvation lipoprotein
predicted DNA-binding transcriptional regulator
galETK 3.48
galT
galE
galK
galactose-1-phosphate uridylyltransferase
UDP-glucose 4-epimerase
galactokinase
gadE-mdtEF 3.29
mdtF
mdtE
gadE
MdtEF-TolC multidrug efflux pump - permease subunit
MdtEF-TolC multidrug efflux pump - membrane fusion protein
GadE DNA-binding transcriptional activator
ydeP 2.34
ydeP
acid resistance protein
fes-ybdZ-entF-fepE 2.26
ybdZ
fes
fepE
entF
MbtH-like protein that enhances the catalytic function of EntF
enterochelin esterase
ferric enterobactin (enterochelin) transport
apo-serine activating enzyme

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
21.8 87.2 GO:0019646 aerobic electron transport chain(GO:0019646)
14.1 42.2 GO:0035999 tetrahydrofolate interconversion(GO:0035999)
10.2 30.6 GO:0009437 carnitine metabolic process(GO:0009437)
7.7 15.5 GO:0015697 quaternary ammonium group transport(GO:0015697) amino-acid betaine transport(GO:0015838)
7.3 21.8 GO:0031346 positive regulation of cell projection organization(GO:0031346)
7.0 28.1 GO:1901654 response to methylglyoxal(GO:0051595) response to ketone(GO:1901654)
6.2 18.5 GO:0006527 arginine catabolic process(GO:0006527)
5.9 17.8 GO:0009297 pilus assembly(GO:0009297)
5.3 21.3 GO:0009607 defense response(GO:0006952) response to biotic stimulus(GO:0009607) response to virus(GO:0009615) response to external biotic stimulus(GO:0043207) response to other organism(GO:0051707) RNA phosphodiester bond hydrolysis(GO:0090501)
5.3 36.8 GO:0071806 protein transmembrane transport(GO:0071806)
4.5 13.4 GO:0019577 aldaric acid metabolic process(GO:0019577) aldaric acid catabolic process(GO:0019579)
4.4 13.3 GO:0046100 purine nucleobase catabolic process(GO:0006145) purine nucleobase biosynthetic process(GO:0009113) hypoxanthine metabolic process(GO:0046100)
4.4 13.3 GO:0031640 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)
3.6 17.8 GO:0071468 cellular response to acidic pH(GO:0071468)
3.5 14.2 GO:0033499 galactose catabolic process via UDP-galactose(GO:0033499)
2.8 11.2 GO:0046385 2'-deoxyribonucleotide biosynthetic process(GO:0009265) deoxyribose phosphate biosynthetic process(GO:0046385)
2.6 15.5 GO:0071978 bacterial-type flagellum-dependent swarming motility(GO:0071978)
2.4 9.6 GO:0051053 negative regulation of DNA replication(GO:0008156) negative regulation of DNA metabolic process(GO:0051053)
2.4 14.2 GO:0010043 response to zinc ion(GO:0010043)
2.4 21.2 GO:0006855 drug transmembrane transport(GO:0006855)
2.3 18.3 GO:0015766 disaccharide transport(GO:0015766) disaccharide catabolic process(GO:0046352)
2.2 11.2 GO:0071229 cellular response to acid chemical(GO:0071229)
1.8 5.5 GO:0031329 regulation of cellular catabolic process(GO:0031329) regulation of cellular carbohydrate catabolic process(GO:0043471)
1.5 79.2 GO:1903508 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)
1.2 6.1 GO:0006972 hyperosmotic response(GO:0006972)
0.8 2.3 GO:0019540 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 4.8 GO:0006310 DNA recombination(GO:0006310)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
29.1 87.2 GO:0070069 cytochrome complex(GO:0070069)
4.6 18.3 GO:0043227 membrane-bounded organelle(GO:0043227) intracellular membrane-bounded organelle(GO:0043231)
3.3 13.3 GO:0005576 extracellular region(GO:0005576)
2.5 17.8 GO:0042995 cell projection(GO:0042995)
0.5 178.2 GO:0005886 plasma membrane(GO:0005886)
0.2 9.5 GO:0042597 periplasmic space(GO:0042597)
0.2 5.5 GO:0019867 outer membrane(GO:0019867)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
29.1 87.2 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)
10.6 42.2 GO:0016882 cyclo-ligase activity(GO:0016882)
6.8 13.7 GO:0015651 amino-acid betaine transmembrane transporter activity(GO:0015199) quaternary ammonium group transmembrane transporter activity(GO:0015651)
6.1 18.3 GO:0016413 O-acetyltransferase activity(GO:0016413) oligosaccharide binding(GO:0070492)
5.3 21.3 GO:0008821 crossover junction endodeoxyribonuclease activity(GO:0008821) endodeoxyribonuclease activity, producing 3'-phosphomonoesters(GO:0016889)
5.2 15.5 GO:0005275 amine transmembrane transporter activity(GO:0005275) transmembrane receptor activity(GO:0099600)
4.4 13.3 GO:0004096 catalase activity(GO:0004096)
4.4 17.8 GO:0044183 protein binding involved in protein folding(GO:0044183)
4.4 21.8 GO:0001141 transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding(GO:0001141) bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding(GO:0001217)
3.9 11.6 GO:0015101 organic cation transmembrane transporter activity(GO:0015101)
3.5 14.2 GO:0003978 UDP-glucose 4-epimerase activity(GO:0003978)
3.3 13.4 GO:0016662 oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor(GO:0016662)
3.1 6.2 GO:0051087 chaperone binding(GO:0051087)
2.0 6.1 GO:0051920 peroxiredoxin activity(GO:0051920)
1.2 81.1 GO:0003700 transcription factor activity, sequence-specific DNA binding(GO:0003700)
1.1 2.3 GO:0015620 ferric-enterobactin transmembrane transporter activity(GO:0015620)
1.0 18.5 GO:0016831 carboxy-lyase activity(GO:0016831)
0.6 20.3 GO:0008233 peptidase activity(GO:0008233)
0.5 16.1 GO:0016836 hydro-lyase activity(GO:0016836)
0.4 11.2 GO:0051539 4 iron, 4 sulfur cluster binding(GO:0051539)
0.3 3.3 GO:0015238 drug transmembrane transporter activity(GO:0015238)
0.2 3.5 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds(GO:0004553)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
14.1 42.2 REACTOME NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX Genes involved in Nonsense Mediated Decay Enhanced by the Exon Junction Complex
2.3 2.3 REACTOME DEVELOPMENTAL BIOLOGY Genes involved in Developmental Biology
1.4 14.2 REACTOME METABOLISM OF CARBOHYDRATES Genes involved in Metabolism of carbohydrates