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

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Results for FNR

Z-value: 1.08

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
fnr0.689.5e-05Click!

Activity profile of FNR motif

Sorted Z-values of FNR motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
rpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ 14.06
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
rpsP-rimM-trmD-rplS 13.18
rplS
rimM
trmD
rpsP
50S ribosomal subunit protein L19
ribosome maturation protein
tRNA m1G37 methyltransferase
30S ribosomal subunit protein S16
rplM-rpsI 13.13
rplM
rpsI
50S ribosomal subunit protein L13
30S ribosomal subunit protein S9
nuoABCEFGHIJKLMN 9.40
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
malPQ 9.10
malP
malQ
maltodextrin phosphorylase
amylomaltase/amylomaltase/amylomaltase
sucABCD 8.96
sucA
sucC
sucB
sucD
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
succinyl-CoA synthetase, β subunit
dihydrolipoyltranssuccinylase
succinyl-CoA synthetase, α subunit
aspC 8.87
aspC
aspartate aminotransferase, PLP-dependent
rplT 8.69
rplT
50S ribosomal subunit protein L20
rplT-pheM 8.68
rplT
pheM
50S ribosomal subunit protein L20
phenylalanyl-tRNA synthetase (pheST) operon leader peptide
aceEF 8.42
aceF
aceE
pyruvate dehydrogenase, E2 subunit
subunit of E1p component of pyruvate dehydrogenase complex
dppABCDF 8.05
dppA
dppB
dppC
dppD
dppF
dipeptide ABC transporter - periplasmic binding protein
dipeptide ABC transporter - predicted membrane subunit
dipeptide ABC transporter - predicted membrane subunit
dipeptide ABC transporter - predicted ATP binding subunit
dipeptide ABC transporter - predicted ATP binding subunit
sucAB 7.55
sucA
sucB
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
dihydrolipoyltranssuccinylase
adhE 6.69
adhE
aldehyde-alcohol dehydrogenase
lpd 6.46
lpd
lipoamide dehydrogenase
yecR 6.35
yecR
predicted protein
gltBDF 6.27
gltB
gltD
gltF
glutamate synthase, large subunit
glutamate synthase, small subunit
periplasmic protein
puuAP 6.17
puuP
puuA
putrescine:H+ symporter PuuP
glutamate-putrescine ligase
sdhCDAB-sucABCD 6.10
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
upp-uraA 5.95
upp
uraA
uracil phosphoribosyltransferase
uracil:H+ symporter UraA
ndh 5.85
ndh
NADH:quinone oxidoreductase II
sodA 5.00
sodA
superoxide dismutase (Mn)
ysgA 4.85
ysgA
predicted hydrolase
pdhR-aceEF-lpd 4.33
pdhR
lpd
aceF
aceE
PdhR DNA-binding transcriptional dual regulator
lipoamide dehydrogenase
pyruvate dehydrogenase, E2 subunit
subunit of E1p component of pyruvate dehydrogenase complex
gdhA 4.28
gdhA
glutamate dehydrogenase
gcvTHP 3.85
gcvH
gcvP
gcvT
glycine cleavage system H protein
glycine decarboxylase
aminomethyltransferase
hemA-prfA-prmC 3.79
hemA
prfA
prmC
glutamyl-tRNA reductase
peptide chain release factor RF1
protein-(glutamine-N5) methyltransferase
focA-pflB 3.77
focA
pflB
formate channel FocA
pyruvate formate-lyase (inactive)
nirBDC-cysG 3.75
nirD
cysG
nirC
nirB
nitrite reductase, small subunit
siroheme synthase subunit
nitrite transporter NirC
nitrite reductase, large subunit
glnK-amtB 3.71
glnK
amtB
nitrogen regulatory protein GlnK
ammonia / ammonium transporter
gadAX 3.43
gadX
gadA
GadX DNA-binding transcriptional dual regulator
glutamate decarboxylase A subunit
tpx 3.37
tpx
lipid hydroperoxide peroxidase
ynfEFGH-dmsD 3.31
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
cydDC 3.24
cydC
cydD
glutathione / L-cysteine exporter - CydC subunit
glutathione / L-cysteine exporter - CydD subunit
grcA 3.22
grcA
stress-induced alternate pyruvate formate-lyase subunit
gnd 3.16
gnd
6-phosphogluconate dehydrogenase, decarboxylating
moeAB 2.95
moeB
moeA
molybdopterin-synthase adenylyltransferase
molybdopterin molybdenumtransferase
katG 2.79
katG
hydroperoxidase I
cydAB 2.68
cydA
cydB
cytochrome bd-I terminal oxidase subunit I
cytochrome bd-I terminal oxidase subunit II
cyoABCDE 2.62
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
bcsBZ 2.35
bcsB
bcsZ
cellulose synthase, periplasmic subunit
endo-1,4-D-glucanase
zwf 1.86
zwf
glucose-6-phosphate dehydrogenase (NADP+)
ubiCA 1.85
ubiC
ubiA
chorismate lyase
4-hydroxybenzoate octaprenyltransferase
fdhF 1.84
fdhF
formate dehydrogenase H
pitA 1.84
pitA
metal phosphate:H+ symporter PitA
nrfABCDEFG 1.38
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
pstSCAB-phoU 1.33
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
ackA 1.11
ackA
acetate kinase
aspA-dcuA 1.07
aspA
dcuA
aspartate ammonia-lyase
dicarboxylate transporter DcuA
aspA 0.90
aspA
aspartate ammonia-lyase
ompX 0.84
ompX
outer membrane protein X
hyfABCDEFGHIJR-focB 0.51
hyfJ
hyfI
hyfH
hyfC
hyfB
hyfA
hyfG
hyfF
hyfE
hyfD
hyfR
focB
hydrogenase 4 component J, putative protein processing element
hydrogenase 4, small subunit
hydrogenase 4, component H
hydrogenase 4, component C
hydrogenase 4, component B
hydrogenase 4, component A
hydrogenase 4, large subunit
hydrogenase 4, component F
hydrogenase 4, component E
hydrogenase 4, component D
HyfR DNA-binding transcriptional activator
FocB formate FNT transporter
yqjI 0.50
yqjI
YqjI DNA-binding transcriptional repressor
napFDAGHBC-ccmABCDEFGH 0.40
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
norVW 0.23
norW
norV
NADH:flavorubredoxin reductase
flavorubredoxin
dpiBA 0.19
dpiB
dpiA
DpiB sensory histidine kinase
DpiA transcriptional dual regulator
soxS 0.19
soxS
SoxS DNA-binding transcriptional dual regulator
nikABCDER 0.16
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

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
5.3 26.3 GO:0030490 maturation of SSU-rRNA(GO:0030490)
4.9 14.6 GO:0019464 glycine decarboxylation via glycine cleavage system(GO:0019464)
4.7 14.1 GO:0060701 negative regulation of nuclease activity(GO:0032074) negative regulation of ribonuclease activity(GO:0060701) negative regulation of endoribonuclease activity(GO:0060702)
4.2 8.4 GO:0035383 acyl-CoA metabolic process(GO:0006637) thioester metabolic process(GO:0035383)
3.8 11.3 GO:0035672 oligopeptide transport(GO:0006857) oligopeptide transmembrane transport(GO:0035672)
3.0 9.1 GO:0030978 alpha-glucan metabolic process(GO:0030978) alpha-glucan catabolic process(GO:0030980)
3.0 12.0 GO:1902600 hydrogen ion transmembrane transport(GO:1902600)
3.0 8.9 GO:0046417 chorismate metabolic process(GO:0046417)
2.8 8.5 GO:0019646 aerobic electron transport chain(GO:0019646)
2.2 17.4 GO:0042273 ribosomal large subunit assembly(GO:0000027) ribosomal large subunit biogenesis(GO:0042273)
2.1 6.3 GO:0019676 ammonia assimilation cycle(GO:0019676)
2.1 6.2 GO:0015847 polyamine transport(GO:0015846) putrescine transport(GO:0015847)
2.0 6.0 GO:0043174 pyrimidine nucleobase transport(GO:0015855) nucleoside salvage(GO:0043174)
1.7 5.0 GO:0006801 response to superoxide(GO:0000303) superoxide metabolic process(GO:0006801)
1.6 7.9 GO:0017004 cytochrome complex assembly(GO:0017004)
1.3 8.1 GO:0006536 glutamate metabolic process(GO:0006536)
1.1 1.1 GO:0006083 acetate metabolic process(GO:0006083)
1.1 5.4 GO:0006567 threonine catabolic process(GO:0006567)
0.9 3.8 GO:0006783 heme biosynthetic process(GO:0006783) heme metabolic process(GO:0042168)
0.9 3.4 GO:0051454 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)
0.7 2.2 GO:0006067 ethanol metabolic process(GO:0006067)
0.6 1.9 GO:0006808 regulation of nitrogen utilization(GO:0006808) nitrogen utilization(GO:0019740)
0.6 3.2 GO:0046177 D-gluconate metabolic process(GO:0019521) D-gluconate catabolic process(GO:0046177)
0.6 1.9 GO:0009372 quorum sensing(GO:0009372)
0.6 1.8 GO:0015710 tellurite transport(GO:0015710)
0.5 6.2 GO:0006099 tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101)
0.4 1.9 GO:0006743 ubiquinone metabolic process(GO:0006743) ubiquinone biosynthetic process(GO:0006744) ketone biosynthetic process(GO:0042181) quinone metabolic process(GO:1901661) quinone biosynthetic process(GO:1901663)
0.3 1.0 GO:0046039 GTP metabolic process(GO:0046039)
0.3 1.3 GO:2000186 regulation of phosphate transport(GO:0010966) cellular anion homeostasis(GO:0030002) cellular monovalent inorganic anion homeostasis(GO:0030320) cellular phosphate ion homeostasis(GO:0030643) negative regulation of transporter activity(GO:0032410) negative regulation of ion transmembrane transporter activity(GO:0032413) negative regulation of transmembrane transport(GO:0034763) negative regulation of ion transmembrane transport(GO:0034766) negative regulation of ion transport(GO:0043271) regulation of anion transport(GO:0044070) phosphate ion homeostasis(GO:0055062) anion homeostasis(GO:0055081) monovalent inorganic anion homeostasis(GO:0055083) cellular divalent inorganic anion homeostasis(GO:0072501) cellular trivalent inorganic anion homeostasis(GO:0072502) divalent inorganic anion homeostasis(GO:0072505) trivalent inorganic anion homeostasis(GO:0072506) negative regulation of anion transport(GO:1903792) regulation of inorganic anion transmembrane transport(GO:1903795) negative regulation of inorganic anion transmembrane transport(GO:1903796) regulation of anion transmembrane transport(GO:1903959) negative regulation of anion transmembrane transport(GO:1903960) regulation of phosphate transmembrane transport(GO:2000185) negative regulation of phosphate transmembrane transport(GO:2000186)
0.1 1.6 GO:0034599 cellular response to oxidative stress(GO:0034599)
0.1 0.2 GO:0071310 cellular response to organic substance(GO:0071310)
0.0 0.2 GO:0015833 peptide transport(GO:0015833)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
7.5 22.6 GO:0045252 tricarboxylic acid cycle enzyme complex(GO:0045239) dihydrolipoyl dehydrogenase complex(GO:0045240) oxoglutarate dehydrogenase complex(GO:0045252)
4.1 57.7 GO:0022625 large ribosomal subunit(GO:0015934) cytosolic large ribosomal subunit(GO:0022625)
1.8 5.3 GO:0070069 cytochrome complex(GO:0070069)
1.6 6.2 GO:0070469 respiratory chain(GO:0070469) plasma membrane respiratory chain(GO:0070470) respiratory chain complex(GO:0098803)
0.8 3.2 GO:0005576 extracellular region(GO:0005576)
0.7 10.5 GO:1990204 oxidoreductase complex(GO:1990204)
0.4 5.0 GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing(GO:0055052)
0.3 3.7 GO:0031234 extrinsic component of cytoplasmic side of plasma membrane(GO:0031234)
0.2 1.3 GO:0019897 extrinsic component of plasma membrane(GO:0019897)
0.1 31.5 GO:0005829 cytosol(GO:0005829)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
7.5 22.6 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)
5.5 16.6 GO:0031405 lipoic acid binding(GO:0031405)
5.5 43.7 GO:0070180 large ribosomal subunit rRNA binding(GO:0070180)
5.3 15.8 GO:0008137 NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
4.7 14.1 GO:0030371 translation repressor activity(GO:0030371) translation regulator activity(GO:0045182)
3.0 9.1 GO:0004133 glycogen debranching enzyme activity(GO:0004133)
2.7 8.1 GO:0035673 oligopeptide transporter activity(GO:0015198) oligopeptide transmembrane transporter activity(GO:0035673)
2.1 10.6 GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors(GO:0016638)
2.0 6.0 GO:0005350 pyrimidine nucleobase transmembrane transporter activity(GO:0005350)
1.7 5.0 GO:0016721 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
1.3 5.4 GO:0008861 formate C-acetyltransferase activity(GO:0008861)
1.3 2.6 GO:0048038 quinone binding(GO:0048038) ubiquinone binding(GO:0048039)
1.3 3.8 GO:0004325 ferrochelatase activity(GO:0004325)
1.1 3.4 GO:0051920 peroxiredoxin activity(GO:0051920)
1.1 8.8 GO:0008519 ammonium transmembrane transporter activity(GO:0008519)
1.1 6.5 GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor(GO:0016668)
0.9 2.8 GO:0004096 catalase activity(GO:0004096)
0.9 2.7 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)
0.8 3.8 GO:0008276 protein methyltransferase activity(GO:0008276)
0.7 1.4 GO:0016662 oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor(GO:0016662)
0.6 1.9 GO:0004659 prenyltransferase activity(GO:0004659)
0.6 1.8 GO:0005385 zinc ion transmembrane transporter activity(GO:0005385) tellurite transmembrane transporter activity(GO:0015118) tellurite uptake transmembrane transporter activity(GO:0015654)
0.5 3.2 GO:0005319 lipid transporter activity(GO:0005319)
0.5 8.9 GO:0008483 transaminase activity(GO:0008483)
0.4 2.0 GO:0016841 ammonia-lyase activity(GO:0016841)
0.4 2.9 GO:0070566 adenylyltransferase activity(GO:0070566)
0.3 3.9 GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor(GO:0016620)
0.2 1.1 GO:0016774 phosphotransferase activity, carboxyl group as acceptor(GO:0016774)
0.2 3.4 GO:0016831 carboxy-lyase activity(GO:0016831)
0.1 0.4 GO:0005048 signal sequence binding(GO:0005048)
0.1 2.3 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds(GO:0004553)
0.1 2.8 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor(GO:0016616)
0.1 0.2 GO:0015099 nickel cation transmembrane transporter activity(GO:0015099)
0.1 1.2 GO:0030145 manganese ion binding(GO:0030145)
0.1 0.2 GO:0001108 basal transcription machinery binding(GO:0001098) bacterial-type RNA polymerase holo enzyme binding(GO:0001108)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
2.0 6.1 REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE Genes involved in Pyruvate metabolism and Citric Acid (TCA) cycle