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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for Fur

Z-value: 3.17

Transcription factors associated with Fur

Gene Symbol Gene ID Gene Info
fur
fur Fur transcriptional dual regulator

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
fur-0.991.8e-06Click!

Activity profile of Fur motif

Sorted Z-values of Fur motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
cirA 15.09
cirA
outer membrane receptor involved in uptake of ferric dihyroxybenzoylserine
yjjZ 12.58
yjjZ
predicted protein
entCEBAH 10.82
entA
entH
entC
entB
entE
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
proofreading thioesterase in enterobactin biosynthesis
isochorismate synthase 1
EntB
2,3-dihydroxybenzoate-AMP ligase
fhuF 10.46
fhuF
hydroxamate siderophore iron reductase
feoABC 10.24
feoB
feoC
feoA
Fe2+ transporter FeoB
predicted DNA-binding transcriptional regulator
ferrous iron transport protein A
fecIR 10.23
fecR
fecI
regulator for fec operon, periplasmic
RNA polymerase, sigma 19 factor
fes-ybdZ-entF-fepE 9.32
ybdZ
fes
fepE
entF
MbtH-like protein that enhances the catalytic function of EntF
enterochelin esterase
ferric enterobactin (enterochelin) transport
apo-serine activating enzyme
exbBD 9.27
exbB
exbD
TonB energy transducing system - ExbB subunit
tonB energy transducing system - ExbD subunit
sufABCDSE 9.05
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
tonB 8.96
tonB
TonB energy transducing system - TonB subunit
fepA-entD 8.60
fepA
entD
ferric enterobactin / colicin B / colicin D outer membrane porin FepA
phosphopantetheinyl transferase/phosphopantetheinyl transferase
exbD 8.04
exbD
tonB energy transducing system - ExbD subunit
fhuE 7.58
fhuE
ferric coprogen outer membrane porin FhuE
fepB 6.75
fepB
ferric enterobactin ABC transporter - periplasmic binding protein
yqjH 6.65
yqjH
ferric reductase, NADPH-dependent
fhuACDB 6.27
fhuD
fhuA
fhuC
fhuB
iron (III) hydroxamate ABC transporter - periplasmic binding protein
ferrichrome / phage / antibiotic outer membrane porin FhuA
iron (III) hydroxamate ABC transporter - ATP binding subunit
iron (III) hydroxamate ABC transporter - membrane subunit
nrdHIEF 6.18
nrdH
nrdI
nrdE
nrdF
glutaredoxin-like protein
flavodoxin involved in dimanganese-tyrosyl radical cofactor maintenance for ribonucleotide reductase
ribonucleoside-diphosphate reductase 2, α subunit
ribonucleoside-diphosphate reductase 2, β subunit
fecABCDE 5.94
fecD
fecE
fecB
fecC
fecA
ferric citrate ABC transporter - membrane subunit
ferric citrate ABC transporter - ATP binding subunit
ferric citrate ABC transporter - periplasmic binding protein
ferric citrate ABC transporter - membrane subunit
ferric citrate outer membrane porin FecA
fepDGC 4.72
fepC
fepG
fepD
ferric enterobactin ABC transporter - ATP binding subunit
ferric enterobactin ABC transporter - membrane subunit
ferric enterobactin ABC transporter - membrane subunit
mntH 4.60
mntH
Mn2+ / Fe2+: H+ symporter MntH
entS 3.76
entS
enterobactin exporter EntS
fiu 2.82
fiu
putative outer membrane receptor for iron transport
glnK-amtB 2.55
glnK
amtB
nitrogen regulatory protein GlnK
ammonia / ammonium transporter
ryhB 2.28
ryhB
RyhB
katE 2.03
katE
catalase II
gpmA 1.79
gpmA
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
nac 1.59
nac
Nac DNA-binding transcriptional dual regulator
soxS 1.13
soxS
SoxS DNA-binding transcriptional dual regulator
ygaC 0.98
ygaC
predicted protein
zinT 0.97
zinT
cadmium-induced cadmium binding protein
gdhA 0.89
gdhA
glutamate dehydrogenase
garPLRK-rnpB 0.87
garL
rnpB
garR
garK
garP
α-dehydro-β-deoxy-D-glucarate aldolase
RnpB
tartronate semialdehyde reductase
glycerate kinase I
galactarate / glucarate / glycerate transporter GarP
cyoABCDE 0.82
cyoA
cyoC
cyoB
cyoE
cyoD
cytochrome bo terminal oxidase subunit II
cytochrome bo terminal oxidase subunit III
cytochrome bo terminal oxidase subunit I
heme O synthase
cytochrome bo terminal oxidase subunit IV
sodA 0.73
sodA
superoxide dismutase (Mn)
soxR 0.54
soxR
SoxR DNA-binding transcriptional dual regulator
grcA 0.43
grcA
stress-induced alternate pyruvate formate-lyase subunit
gspCDEFGHIJKLMO 0.38
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
nohA-ydfN-tfaQ 0.31
nohA
tfaQ
ydfN
Qin prophage; predicted packaging protein
Qin prophage; predicted tail fibre assembly protein
Qin prophage; predicted side tail fibre assembly protein

Network of associatons between targets according to the STRING database.

First level regulatory network of Fur

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
9.6 28.7 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)
8.0 32.2 GO:0033212 iron assimilation(GO:0033212)
6.8 47.8 GO:0006826 iron ion transport(GO:0006826)
3.9 15.5 GO:0015891 siderophore transport(GO:0015891)
1.7 15.2 GO:0043085 positive regulation of catalytic activity(GO:0043085)
1.6 8.0 GO:0050821 protein stabilization(GO:0050821)
0.6 1.8 GO:0031329 regulation of glucose metabolic process(GO:0010906) regulation of cellular catabolic process(GO:0031329) regulation of cellular carbohydrate catabolic process(GO:0043471)
0.3 1.0 GO:0046686 response to cadmium ion(GO:0046686)
0.3 2.0 GO:0006972 hyperosmotic response(GO:0006972)
0.3 0.9 GO:0019579 aldaric acid metabolic process(GO:0019577) aldaric acid catabolic process(GO:0019579)
0.3 2.6 GO:0015696 ammonium transport(GO:0015696)
0.2 0.7 GO:0000303 response to superoxide(GO:0000303) superoxide metabolic process(GO:0006801)
0.2 0.8 GO:1902600 hydrogen ion transmembrane transport(GO:1902600)
0.1 0.4 GO:0006567 threonine catabolic process(GO:0006567)
0.1 0.5 GO:0006536 glutamate metabolic process(GO:0006536)
0.0 0.4 GO:0071806 protein transmembrane transport(GO:0071806)
0.0 0.8 GO:0045892 negative regulation of transcription, DNA-templated(GO:0045892) negative regulation of RNA biosynthetic process(GO:1902679) negative regulation of nucleic acid-templated transcription(GO:1903507)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.1 8.6 GO:0045203 integral component of cell outer membrane(GO:0045203)
0.9 9.8 GO:0071575 integral component of external side of plasma membrane(GO:0071575)
0.9 10.7 GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing(GO:0055052)
0.6 27.3 GO:0009279 cell outer membrane(GO:0009279)
0.3 10.3 GO:0098797 plasma membrane protein complex(GO:0098797)
0.3 4.1 GO:1990204 oxidoreductase complex(GO:1990204)
0.2 9.3 GO:0043234 protein complex(GO:0043234)
0.1 7.1 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)
0.1 31.1 GO:0005886 plasma membrane(GO:0005886)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
8.8 53.0 GO:0042927 siderophore transmembrane transporter activity(GO:0015343) siderophore transporter activity(GO:0042927)
8.7 17.3 GO:0031992 energy transducer activity(GO:0031992)
8.1 16.2 GO:0005381 iron ion transmembrane transporter activity(GO:0005381)
3.6 10.8 GO:0016803 hydrolase activity, acting on ether bonds(GO:0016801) ether hydrolase activity(GO:0016803) phosphopantetheine binding(GO:0031177)
2.1 6.2 GO:0016728 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor(GO:0004748) oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor(GO:0016728) ribonucleoside-diphosphate reductase activity(GO:0061731)
1.5 9.0 GO:0016783 sulfurtransferase activity(GO:0016783)
0.6 7.9 GO:0051537 2 iron, 2 sulfur cluster binding(GO:0051537)
0.6 5.4 GO:0015078 hydrogen ion transmembrane transporter activity(GO:0015078)
0.4 1.1 GO:0001108 basal transcription machinery binding(GO:0001098) bacterial-type RNA polymerase holo enzyme binding(GO:0001108)
0.4 1.8 GO:0016868 intramolecular transferase activity, phosphotransferases(GO:0016868)
0.3 2.6 GO:0008519 ammonium transmembrane transporter activity(GO:0008519)
0.3 0.9 GO:0016662 oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor(GO:0016662)
0.3 3.2 GO:0071949 FAD binding(GO:0071949)
0.2 0.7 GO:0004784 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
0.1 0.4 GO:0008861 formate C-acetyltransferase activity(GO:0008861)
0.1 0.5 GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors(GO:0016638)
0.0 0.4 GO:0008233 peptidase activity(GO:0008233)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
3.1 9.3 PID ANGIOPOIETIN RECEPTOR PATHWAY Angiopoietin receptor Tie2-mediated signaling

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
3.1 9.3 REACTOME DEVELOPMENTAL BIOLOGY Genes involved in Developmental Biology