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

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Results for ArcA

Z-value: 1.26

Transcription factors associated with ArcA

Gene Symbol Gene ID Gene Info
arcA
arcA ArcA transcriptional dual regulator

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
arcA0.481.1e-02Click!

Activity profile of ArcA motif

Sorted Z-values of ArcA motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
rpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ 13.32
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
nuoABCEFGHIJKLMN 10.79
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
sucABCD 9.99
sucA
sucC
sucB
sucD
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
succinyl-CoA synthetase, β subunit
dihydrolipoyltranssuccinylase
succinyl-CoA synthetase, α subunit
aceEF 8.58
aceF
aceE
pyruvate dehydrogenase, E2 subunit
subunit of E1p component of pyruvate dehydrogenase complex
sucAB 8.51
sucA
sucB
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
dihydrolipoyltranssuccinylase
sdhCDAB-sucABCD 8.05
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
lpd 7.53
lpd
lipoamide dehydrogenase
acnB 7.36
acnB
bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase
icd 6.92
icd
isocitrate dehydrogenase
oppABCDF 6.86
oppA
oppC
oppB
oppD
oppF
peptide ABC transporter - periplasmic binding protein
murein tripeptide ABC transporter / peptide ABC transporter - putative membrane subunit
murein tripeptide ABC transporter / peptide ABC transporter - putative membrane subunit
murein tripeptide ABC transporter / peptide ABC transporter - putative ATP binding subunit
murein tripeptide ABC transporter / peptide ABC transporter - putative ATP binding subunit
gltA 6.67
gltA
citrate synthase
mdh 6.27
mdh
malate dehydrogenase
tpx 5.79
tpx
lipid hydroperoxide peroxidase
puuAP 5.30
puuP
puuA
putrescine:H+ symporter PuuP
glutamate-putrescine ligase
puuDRCBE 4.90
puuR
puuC
puuB
puuD
puuE
PuuR DNA-binding transcriptional repressor
γ-glutamyl-γ-aminobutyraldehyde dehydrogenase
γ-glutamylputrescine oxidase
γ-glutamyl-γ-aminobutyrate hydrolase
4-aminobutyrate aminotransferase
sodA 4.50
sodA
superoxide dismutase (Mn)
ptsG 3.74
ptsG
glucose PTS permease - PtsG subunit
rpoS 3.50
rpoS
RNA polymerase, sigma S (sigma 38) factor
lldPRD 3.41
lldP
lldR
lldD
(R)-lactate / (S)-lactate / glycolate:H+ symporter LldP
LldR transcriptional dual regulator
L-lactate dehydrogenase
ubiCA 3.24
ubiC
ubiA
chorismate lyase
4-hydroxybenzoate octaprenyltransferase
uvrA 3.16
uvrA
excision nuclease subunit A
ndh 3.01
ndh
NADH:quinone oxidoreductase II
gadAX 2.94
gadX
gadA
GadX DNA-binding transcriptional dual regulator
glutamate decarboxylase A subunit
hemA-prfA-prmC 2.77
hemA
prfA
prmC
glutamyl-tRNA reductase
peptide chain release factor RF1
protein-(glutamine-N5) methyltransferase
cyoABCDE 2.74
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
cydAB 2.70
cydA
cydB
cytochrome bd-I terminal oxidase subunit I
cytochrome bd-I terminal oxidase subunit II
moeAB 2.63
moeB
moeA
molybdopterin-synthase adenylyltransferase
molybdopterin molybdenumtransferase
fadBA 2.29
fadB
fadA
dodecenoyl-CoA δ-isomerase, enoyl-CoA hydratase, 3-hydroxybutyryl-CoA epimerase, 3-hydroxyacyl-CoA dehydrogenase
3-ketoacyl-CoA thiolase
fadIJ 2.20
fadJ
fadI
FadJ component of anaerobic fatty acid oxidation complex
FadI component of anaerobic fatty acid oxidation complex
fumA 1.94
fumA
fumarase A
betIBA 1.85
betB
betI
betA
betaine aldehyde dehydrogenase
BetI DNA-binding transcriptional repressor
choline dehydrogenase
cydDC 1.50
cydC
cydD
glutathione / L-cysteine exporter - CydC subunit
glutathione / L-cysteine exporter - CydD subunit
fumAC 1.43
fumA
fumC
fumarase A
fumarase C
grcA 1.34
grcA
stress-induced alternate pyruvate formate-lyase subunit
aldA 1.01
aldA
aldehyde dehydrogenase A
focA-pflB 0.94
focA
pflB
formate channel FocA
pyruvate formate-lyase (inactive)
appCBXA 0.90
appC
appB
appA
appX
cytochrome bd-II terminal oxidase subunit I
cytochrome bd-II terminal oxidase subunit II
periplasmic protein with phosphoanhydride phosphatase and multiple inositol-polyphosphate phosphatase activity
small outer membrane protein
fadH 0.87
fadH
2,4-dienoyl-CoA reductase
arcZ 0.62
arcZ
ArcZ
hybOABCDEFG 0.48
hybG
hybF
hybE
hybD
hybC
hybB
hybA
hybO
hydrogenase 2 accessory protein
protein involved with the maturation of hydrogenases 1 and 2
hydrogenase 2-specific chaperone
predicted maturation peptidase for hydrogenase 2
hydrogenase 2, large subunit
hydrogenase 2 - integral membrane subunit HybB
hydrogenase 2 - [Fe-S] binding, ferredoxin-type component HybA
hydrogenase 2, small subunit
hyaABCDEF 0.37
hyaB
hyaC
hyaA
hyaF
hyaD
hyaE
hydrogenase 1, large subunit
hydrogenase 1, b-type cytochrome subunit
hydrogenase 1, small subunit
protein involved in nickel incorporation into hydrogenase 1 proteins
protein involved in processing of HyaA and HyaB proteins
protein involved in quality control of HyaA
fadL 0.31
fadL
long-chain fatty acid outer membrane porin; bacteriophage T2 receptor

Network of associatons between targets according to the STRING database.

First level regulatory network of ArcA

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
4.4 13.3 GO:0060701 negative regulation of nuclease activity(GO:0032074) negative regulation of ribonuclease activity(GO:0060701) negative regulation of endoribonuclease activity(GO:0060702)
3.4 13.5 GO:1902600 hydrogen ion transmembrane transport(GO:1902600)
2.8 8.4 GO:0035672 oligopeptide transport(GO:0006857) oligopeptide transmembrane transport(GO:0035672)
2.5 7.5 GO:0019464 glycine decarboxylation via glycine cleavage system(GO:0019464)
2.5 7.4 GO:0019626 short-chain fatty acid catabolic process(GO:0019626)
2.2 6.6 GO:0019646 aerobic electron transport chain(GO:0019646)
2.1 6.3 GO:0006108 malate metabolic process(GO:0006108)
1.9 21.1 GO:0006099 tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101)
1.8 5.3 GO:0015847 polyamine transport(GO:0015846) putrescine transport(GO:0015847)
1.6 3.2 GO:0006637 acyl-CoA metabolic process(GO:0006637) thioester metabolic process(GO:0035383)
1.5 4.5 GO:0006801 response to superoxide(GO:0000303) superoxide metabolic process(GO:0006801)
1.2 4.9 GO:0006598 polyamine catabolic process(GO:0006598) putrescine catabolic process(GO:0009447)
1.1 4.4 GO:0006004 fucose metabolic process(GO:0006004) fucose catabolic process(GO:0019317) L-fucose metabolic process(GO:0042354) L-fucose catabolic process(GO:0042355)
0.9 3.7 GO:0046323 glucose transport(GO:0015758) glucose import(GO:0046323)
0.9 2.8 GO:0008213 protein methylation(GO:0006479) protein alkylation(GO:0008213)
0.9 3.5 GO:0001121 transcription from bacterial-type RNA polymerase promoter(GO:0001121)
0.9 2.6 GO:0046039 GTP metabolic process(GO:0046039)
0.7 2.9 GO:0051454 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)
0.6 3.2 GO:0042181 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)
0.5 5.8 GO:0034599 cellular response to oxidative stress(GO:0034599)
0.5 2.3 GO:0006567 threonine catabolic process(GO:0006567)
0.3 1.4 GO:0022900 electron transport chain(GO:0022900)
0.2 1.9 GO:0042398 cellular modified amino acid biosynthetic process(GO:0042398)
0.2 0.9 GO:0016485 protein processing(GO:0016485)
0.0 3.2 GO:0009314 response to radiation(GO:0009314)
0.0 0.3 GO:0006869 lipid transport(GO:0006869)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
8.9 26.6 GO:0045239 tricarboxylic acid cycle enzyme complex(GO:0045239) dihydrolipoyl dehydrogenase complex(GO:0045240) oxoglutarate dehydrogenase complex(GO:0045252)
2.7 10.8 GO:0098803 respiratory chain(GO:0070469) plasma membrane respiratory chain(GO:0070470) respiratory chain complex(GO:0098803)
2.1 6.3 GO:0070069 cytochrome complex(GO:0070069)
1.0 13.3 GO:0015934 large ribosomal subunit(GO:0015934) cytosolic large ribosomal subunit(GO:0022625)
0.6 3.2 GO:0009380 excinuclease repair complex(GO:0009380)
0.3 6.8 GO:0019898 extrinsic component of membrane(GO:0019898)
0.2 8.4 GO:0043190 ATP-binding cassette (ABC) transporter complex(GO:0043190) ATPase dependent transmembrane transport complex(GO:0098533) ATPase complex(GO:1904949)
0.1 3.0 GO:0098796 membrane protein complex(GO:0098796)
0.1 0.4 GO:0098567 periplasmic side of plasma membrane(GO:0098567)
0.1 38.8 GO:0005829 cytosol(GO:0005829)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
8.9 26.6 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)
4.6 13.8 GO:0050136 NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
3.3 13.3 GO:0008428 RNA binding transcription factor activity(GO:0001070) transcription antitermination factor activity, RNA binding(GO:0001072) ribonuclease inhibitor activity(GO:0008428)
2.9 8.6 GO:0031405 lipoic acid binding(GO:0031405)
2.3 6.9 GO:0035673 oligopeptide transporter activity(GO:0015198) peptidoglycan transporter activity(GO:0015647) oligopeptide transmembrane transporter activity(GO:0035673)
2.0 6.0 GO:0004659 prenyltransferase activity(GO:0004659)
1.9 5.8 GO:0051920 peroxiredoxin activity(GO:0051920)
1.5 4.5 GO:0016721 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
1.5 4.5 GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity(GO:0003857)
1.3 7.5 GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor(GO:0016668)
1.2 4.9 GO:0003867 4-aminobutyrate transaminase activity(GO:0003867)
1.2 3.6 GO:0016682 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)
1.0 1.0 GO:0004777 succinate-semialdehyde dehydrogenase (NAD+) activity(GO:0004777)
0.9 5.3 GO:0016880 acid-ammonia (or amide) ligase activity(GO:0016880)
0.9 3.5 GO:0001000 bacterial-type RNA polymerase core enzyme binding(GO:0001000)
0.7 2.7 GO:0043879 glycolate transmembrane transporter activity(GO:0043879)
0.6 2.3 GO:0008861 formate C-acetyltransferase activity(GO:0008861)
0.6 2.8 GO:0008276 protein methyltransferase activity(GO:0008276)
0.4 6.4 GO:0003729 mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.4 1.9 GO:0004029 aldehyde dehydrogenase (NAD) activity(GO:0004029)
0.4 2.9 GO:0001140 transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding(GO:0001140)
0.3 6.9 GO:0051287 NAD binding(GO:0051287)
0.3 1.8 GO:0005319 lipid transporter activity(GO:0005319)
0.3 2.6 GO:0070566 adenylyltransferase activity(GO:0070566)
0.1 3.4 GO:0016860 intramolecular oxidoreductase activity(GO:0016860)
0.1 0.4 GO:0005048 signal sequence binding(GO:0005048)
0.1 0.9 GO:0016628 oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor(GO:0016628)
0.1 0.5 GO:1902670 carbon dioxide binding(GO:1902670)
0.1 3.2 GO:0016887 ATPase activity(GO:0016887)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
2.7 8.1 REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT Genes involved in The citric acid (TCA) cycle and respiratory electron transport