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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for FNR

Z-value: 2.69

Transcription factors associated with FNR

Gene Symbol Gene ID Gene Info
fnr
fnr FNR DNA-binding transcriptional dual regulator

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
fnr0.893.3e-03Click!

Activity profile of FNR motif

Sorted Z-values of FNR motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
focA-pflB 14.35
focA
pflB
formate channel FocA
pyruvate formate-lyase (inactive)
fnrS 11.83
fnrS
FnrS
aspA 10.19
aspA
aspartate ammonia-lyase
dcuC 9.33
dcuC
dicarboxylate transporter DcuC
rpsP-rimM-trmD-rplS 8.92
rplS
rimM
trmD
rpsP
50S ribosomal subunit protein L19
ribosome maturation protein
tRNA m1G37 methyltransferase
30S ribosomal subunit protein S16
rpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ 8.33
rpsC
rplV
rplW
rpsJ
rplP
rpsS
rpsQ
rpmC
rplD
rplB
rplC
30S ribosomal subunit protein S3
50S ribosomal subunit protein L22
50S ribosomal subunit protein L23
30S ribosomal subunit protein S10
50S ribosomal subunit protein L16
30S ribosomal subunit protein S19
30S ribosomal subunit protein S17
50S ribosomal subunit protein L29
50S ribosomal subunit protein L4
50S ribosomal subunit protein L2
50S ribosomal subunit protein L3
aspA-dcuA 7.74
aspA
dcuA
aspartate ammonia-lyase
dicarboxylate transporter DcuA
tpx 7.67
tpx
lipid hydroperoxide peroxidase
sucAB 7.53
sucA
sucB
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
dihydrolipoyltranssuccinylase
sucABCD 7.11
sucA
sucC
sucB
sucD
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
succinyl-CoA synthetase, β subunit
dihydrolipoyltranssuccinylase
succinyl-CoA synthetase, α subunit
tdcABCDEFG 7.11
tdcE
tdcD
tdcG
tdcF
tdcA
tdcC
tdcB
2-ketobutyrate formate-lyase/pyruvate formate-lyase 4, inactive
propionate kinase
L-serine deaminase III
predicted enamine/imine deaminase
TdcA DNA-binding transcriptional activator
serine / threonine:H+ symporter TdcC
catabolic threonine dehydratase
frdABCD 6.88
frdA
frdB
frdC
frdD
fumarate reductase flavoprotein
fumarate reductase iron-sulfur protein
fumarate reductase membrane protein
fumarate reductase membrane protein
rplM-rpsI 6.80
rplM
rpsI
50S ribosomal subunit protein L13
30S ribosomal subunit protein S9
rplT 6.71
rplT
50S ribosomal subunit protein L20
fdhF 6.51
fdhF
formate dehydrogenase H
cydAB 6.45
cydA
cydB
cytochrome bd-I terminal oxidase subunit I
cytochrome bd-I terminal oxidase subunit II
hypBCDE 6.26
hypE
hypD
hypC
hypB
hydrogenase maturation protein, carbamoyl dehydratase
HypD, scaffold protein for assembly of the Fe-(CN)2CO cofactor
HypC, protein involved in hydrogenase 3 maturation
accessory protein for nickel incorporation into hydrogenase isoenzymes
rplT-pheM 5.94
rplT
pheM
50S ribosomal subunit protein L20
phenylalanyl-tRNA synthetase (pheST) operon leader peptide
ackA 5.87
ackA
acetate kinase
ompX 5.84
ompX
outer membrane protein X
ansB 5.80
ansB
asparaginase II
sodA 5.70
sodA
superoxide dismutase (Mn)
lpd 5.69
lpd
lipoamide dehydrogenase
pepT 5.63
pepT
peptidase T
hypBCDE-fhlA 5.63
hypE
hypD
fhlA
hypC
hypB
hydrogenase maturation protein, carbamoyl dehydratase
HypD, scaffold protein for assembly of the Fe-(CN)2CO cofactor
FhlA transcriptional activator
HypC, protein involved in hydrogenase 3 maturation
accessory protein for nickel incorporation into hydrogenase isoenzymes
moaABCDE 5.55
moaE
moaD
moaC
moaB
moaA
molybdopterin synthase large subunit
molybdopterin synthase small subunit
cyclic pyranopterin monophosphate synthase
MoaB protein
GTP 3',8'-cyclase
hcp-hcr 5.53
hcr
hcp
NADH oxidoreductase
hybrid-cluster protein
sdhCDAB-sucABCD 5.51
sucA
sucC
sucB
sucD
sdhA
sdhC
sdhB
sdhD
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
succinyl-CoA synthetase, β subunit
dihydrolipoyltranssuccinylase
succinyl-CoA synthetase, α subunit
succinate:quinone oxidoreductase, FAD binding protein
succinate:quinone oxidoreductase, membrane protein SdhC
succinate:quinone oxidoreductase, iron-sulfur cluster binding protein
succinate:quinone oxidoreductase, membrane protein SdhD
aceEF 5.42
aceF
aceE
pyruvate dehydrogenase, E2 subunit
subunit of E1p component of pyruvate dehydrogenase complex
aspC 5.39
aspC
aspartate aminotransferase, PLP-dependent
gnd 5.28
gnd
6-phosphogluconate dehydrogenase, decarboxylating
nrdDG 5.00
nrdD
nrdG
anaerobic ribonucleoside-triphosphate reductase
anaerobic ribonucleoside-triphosphate reductase-activating protein
fnr 4.89
fnr
FNR DNA-binding transcriptional dual regulator
malPQ 4.58
malP
malQ
maltodextrin phosphorylase
amylomaltase/amylomaltase/amylomaltase
soxS 4.54
soxS
SoxS DNA-binding transcriptional dual regulator
ompW 4.43
ompW
outer membrane protein W
fumA 3.56
fumA
fumarase A
garPLRK-rnpB 3.50
garL
rnpB
garR
garK
garP
α-dehydro-β-deoxy-D-glucarate aldolase
RnpB
tartronate semialdehyde reductase
glycerate kinase I
galactarate / glucarate / glycerate transporter GarP
katG 3.44
katG
hydroperoxidase I
adhE 3.23
adhE
aldehyde-alcohol dehydrogenase
pitA 3.16
pitA
metal phosphate:H+ symporter PitA
napFDAGHBC-ccmABCDEFGH 3.15
napG
napF
napD
napC
ccmH
napA
ccmE
ccmD
ccmG
ccmF
ccmA
ccmC
ccmB
napH
napB
ferredoxin-type protein
ferredoxin-type protein
signal peptide-binding chaperone for NapA
periplasmic nitrate reductase, cytochrome c protein
holocytochrome c synthetase - thiol:disulfide oxidoreductase CcmH
large subunit of periplasmic nitrate reductase, molybdoprotein
membrane anchored periplasmic heme chaperone CcmE
ABC complex for formation and release of holoCcmE - membrane subunit CcmD
holocytochrome c synthetase - thiol:disulfide oxidoreductase CcmG
holocytochrome c synthetase - CcmF subunit
ABC complex for formation and release of holoCcmE - ATP binding subunit
ABC complex for formation and release of holoCcmE - membrane subunit CcmC
ABC complex for formation and release of holoCcmE - membrane subunit CcmB
ferredoxin-type protein
subunit of periplasmic nitrate reductase, cytochrome c550 protein
ynfEFGH-dmsD 3.01
ynfG
ynfF
ynfE
dmsD
ynfH
putative selenate reductase, predicted Fe-S subunit
putative selenate reductase, oxidoreductase subunit
putative selenate reductase, oxidoreductase subunit
DMS reductase maturation protein
putative selenate reductase, predicted membrane anchor subunit
fumB 2.90
fumB
fumarase B
nikABCDER 2.86
nikB
nikC
nikA
nikD
nikE
nikR
nickel ABC transporter - membrane subunit
nickel ABC transporter - membrane subunit
nickel ABC transporter - periplasmic binding protein
nickel ABC transporter - ATP binding subunit
nickel ABC transporter - ATP binding subunit
NikR DNA-binding transcriptional repressor, Ni-binding
narK 2.78
narK
nitrate:nitrite antiporter NarK
zwf 2.77
zwf
glucose-6-phosphate dehydrogenase (NADP+)
dcuB-fumB 2.69
fumB
dcuB
fumarase B
dicarboxylate transporter DcuB
fumAC 2.65
fumA
fumC
fumarase A
fumarase C
narGHJI 2.44
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
nuoABCEFGHIJKLMN 2.27
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
gdhA 2.14
gdhA
glutamate dehydrogenase
grcA 2.06
grcA
stress-induced alternate pyruvate formate-lyase subunit
yqjI 1.90
yqjI
YqjI DNA-binding transcriptional repressor
hmp 1.58
hmp
nitric oxide dioxygenase
fdnGHI 1.38
fdnH
fdnI
fdnG
formate dehydrogenase N, β subunit
formate dehydrogenase N, γ subunit
formate dehydrogenase N, α subunit
gltBDF 1.37
gltB
gltD
gltF
glutamate synthase, large subunit
glutamate synthase, small subunit
periplasmic protein
pdhR-aceEF-lpd 1.35
pdhR
lpd
aceF
aceE
PdhR DNA-binding transcriptional dual regulator
lipoamide dehydrogenase
pyruvate dehydrogenase, E2 subunit
subunit of E1p component of pyruvate dehydrogenase complex
glnD 1.25
glnD
PII uridylyltransferase / uridylyl removing enzyme
fumC 1.14
fumC
fumarase C
nrfABCDEFG 1.08
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
gcvTHP 0.89
gcvH
gcvP
gcvT
glycine cleavage system H protein
glycine decarboxylase
aminomethyltransferase
hemA-prfA-prmC 0.87
hemA
prfA
prmC
glutamyl-tRNA reductase
peptide chain release factor RF1
protein-(glutamine-N5) methyltransferase
arcA 0.86
arcA
ArcA transcriptional dual regulator
pstS 0.68
pstS
phosphate ABC transporter - periplasmic binding protein
uxaCA 0.68
uxaA
uxaC
D-altronate dehydratase
D-glucuronate isomerase/D-galacturonate isomerase
pstSCAB-phoU 0.05
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
ndh 0.05
ndh
NADH:quinone oxidoreductase II

Network of associatons between targets according to the STRING database.

First level regulatory network of FNR

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
4.7 23.5 GO:0006567 threonine catabolic process(GO:0006567)
4.3 17.2 GO:0015942 formate metabolic process(GO:0015942)
3.5 7.0 GO:0006103 2-oxoglutarate metabolic process(GO:0006103)
3.2 3.2 GO:0006067 ethanol metabolic process(GO:0006067)
3.1 15.7 GO:0030490 maturation of SSU-rRNA(GO:0030490)
3.1 46.9 GO:0006099 tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101)
3.0 11.9 GO:0018249 protein dehydration(GO:0018249) peptidyl-S-carbamoyl-L-cysteine dehydration(GO:0046892)
2.9 5.9 GO:0019541 acetate metabolic process(GO:0006083) propionate metabolic process(GO:0019541)
2.7 5.4 GO:0006637 acyl-CoA metabolic process(GO:0006637) thioester metabolic process(GO:0035383)
2.3 21.0 GO:0000027 ribosomal large subunit assembly(GO:0000027) ribosomal large subunit biogenesis(GO:0042273)
2.3 6.9 GO:0006113 fermentation(GO:0006113)
2.2 6.7 GO:0046209 nitric oxide metabolic process(GO:0046209) nitric oxide catabolic process(GO:0046210)
1.9 5.8 GO:0006528 asparagine metabolic process(GO:0006528)
1.9 5.7 GO:0006801 response to superoxide(GO:0000303) superoxide metabolic process(GO:0006801)
1.8 5.5 GO:0034214 protein hexamerization(GO:0034214)
1.8 5.4 GO:0046417 chorismate metabolic process(GO:0046417)
1.7 3.4 GO:0072593 reactive oxygen species metabolic process(GO:0072593)
1.6 3.2 GO:0015710 tellurite transport(GO:0015710)
1.5 4.6 GO:0030978 alpha-glucan metabolic process(GO:0030978) alpha-glucan catabolic process(GO:0030980)
1.4 4.2 GO:0017003 protein-heme linkage(GO:0017003) protein-tetrapyrrole linkage(GO:0017006) cytochrome c-heme linkage(GO:0018063)
1.2 5.0 GO:0046385 2'-deoxyribonucleotide biosynthetic process(GO:0009265) deoxyribose phosphate biosynthetic process(GO:0046385)
1.2 2.4 GO:0019645 anaerobic electron transport chain(GO:0019645)
1.2 3.5 GO:0019577 aldaric acid metabolic process(GO:0019577) aldaric acid catabolic process(GO:0019579)
1.1 5.5 GO:0022904 respiratory electron transport chain(GO:0022904)
1.1 5.3 GO:0046177 D-gluconate metabolic process(GO:0019521) D-gluconate catabolic process(GO:0046177)
1.0 2.9 GO:0015675 nickel cation transport(GO:0015675) nickel cation transmembrane transport(GO:0035444)
0.9 2.8 GO:0009372 quorum sensing(GO:0009372)
0.9 0.9 GO:0019464 glycine decarboxylation via glycine cleavage system(GO:0019464)
0.5 4.4 GO:0006536 glutamate metabolic process(GO:0006536)
0.3 4.3 GO:1901698 response to nitrogen compound(GO:1901698)
0.3 3.1 GO:0034599 cellular response to oxidative stress(GO:0034599)
0.2 0.7 GO:0006063 uronic acid metabolic process(GO:0006063)
0.1 4.6 GO:0006518 peptide metabolic process(GO:0006518)
0.0 0.2 GO:0010921 regulation of phosphatase activity(GO:0010921)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
6.7 20.2 GO:0045252 tricarboxylic acid cycle enzyme complex(GO:0045239) dihydrolipoyl dehydrogenase complex(GO:0045240) oxoglutarate dehydrogenase complex(GO:0045252)
3.4 6.9 GO:0045273 respiratory chain complex II(GO:0045273) plasma membrane respiratory chain complex II(GO:0045274)
2.6 36.7 GO:0015934 large ribosomal subunit(GO:0015934) cytosolic large ribosomal subunit(GO:0022625)
2.4 4.7 GO:0070469 respiratory chain(GO:0070469) plasma membrane respiratory chain(GO:0070470) respiratory chain complex(GO:0098803)
1.6 3.2 GO:0031235 intrinsic component of the cytoplasmic side of the plasma membrane(GO:0031235)
1.1 3.2 GO:0070069 cytochrome complex(GO:0070069)
0.3 3.0 GO:0031234 extrinsic component of cytoplasmic side of plasma membrane(GO:0031234)
0.3 123.4 GO:0044444 cytoplasmic part(GO:0044444)
0.2 1.4 GO:0071575 integral component of external side of plasma membrane(GO:0071575)
0.0 1.4 GO:0005622 intracellular(GO:0005622)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
6.7 20.2 GO:0004149 dihydrolipoyllysine-residue succinyltransferase activity(GO:0004149) oxoglutarate dehydrogenase (succinyl-transferring) activity(GO:0004591) oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor(GO:0016624) S-succinyltransferase activity(GO:0016751)
5.9 23.5 GO:0008861 formate C-acetyltransferase activity(GO:0008861)
4.9 19.8 GO:0005469 succinate:fumarate antiporter activity(GO:0005469)
3.5 28.4 GO:0070180 large ribosomal subunit rRNA binding(GO:0070180)
3.4 6.9 GO:0016635 succinate dehydrogenase activity(GO:0000104) oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor(GO:0016635)
3.0 11.9 GO:0070025 carbon monoxide binding(GO:0070025)
2.8 8.3 GO:0045182 translation repressor activity(GO:0030371) translation regulator activity(GO:0045182)
2.6 10.2 GO:0004333 fumarate hydratase activity(GO:0004333)
2.6 7.7 GO:0051920 peroxiredoxin activity(GO:0051920)
2.6 7.7 GO:0031405 lipoic acid binding(GO:0031405)
2.1 6.4 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)
2.0 10.2 GO:0016841 ammonia-lyase activity(GO:0016841)
1.9 5.7 GO:0004784 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
1.9 5.6 GO:0004177 aminopeptidase activity(GO:0004177)
1.8 11.0 GO:0030151 molybdenum ion binding(GO:0030151)
1.7 5.0 GO:0004748 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)
1.6 1.6 GO:0032843 hydroperoxide reductase activity(GO:0032843)
1.5 4.6 GO:0016662 oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor(GO:0016662)
1.5 4.6 GO:0004133 glycogen debranching enzyme activity(GO:0004133)
1.5 4.5 GO:0001098 basal transcription machinery binding(GO:0001098) bacterial-type RNA polymerase holo enzyme binding(GO:0001108)
1.2 2.4 GO:0008940 nitrate reductase activity(GO:0008940)
1.1 3.4 GO:0004096 catalase activity(GO:0004096)
1.1 3.2 GO:0015654 zinc ion transmembrane transporter activity(GO:0005385) tellurite transmembrane transporter activity(GO:0015118) tellurite uptake transmembrane transporter activity(GO:0015654)
1.0 2.9 GO:0015099 nickel cation transmembrane transporter activity(GO:0015099)
0.9 5.7 GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor(GO:0016668)
0.9 5.5 GO:0016783 sulfurtransferase activity(GO:0016783)
0.7 3.5 GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors(GO:0016638)
0.7 5.9 GO:0016774 phosphotransferase activity, carboxyl group as acceptor(GO:0016774)
0.5 5.0 GO:0051537 2 iron, 2 sulfur cluster binding(GO:0051537)
0.5 2.8 GO:0015562 efflux transmembrane transporter activity(GO:0015562)
0.4 5.8 GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides(GO:0016811)
0.3 5.4 GO:0008483 transaminase activity(GO:0008483)
0.3 11.3 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor(GO:0016616)
0.3 1.2 GO:0070569 uridylyltransferase activity(GO:0070569)
0.2 0.9 GO:0008170 N-methyltransferase activity(GO:0008170)
0.1 0.7 GO:0008198 ferrous iron binding(GO:0008198)
0.0 0.2 GO:0042301 phosphate ion binding(GO:0042301)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
1.8 5.5 REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT Genes involved in The citric acid (TCA) cycle and respiratory electron transport