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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for ArcA

Z-value: 0.63

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
arcA0.686.4e-02Click!

Activity profile of ArcA motif

Sorted Z-values of ArcA motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
focA-pflB 1.97
focA
pflB
formate channel FocA
pyruvate formate-lyase (inactive)
sucAB 1.64
sucA
sucB
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
dihydrolipoyltranssuccinylase
sucABCD 1.53
sucA
sucC
sucB
sucD
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
succinyl-CoA synthetase, β subunit
dihydrolipoyltranssuccinylase
succinyl-CoA synthetase, α subunit
dcuC 1.44
dcuC
dicarboxylate transporter DcuC
tpx 1.42
tpx
lipid hydroperoxide peroxidase
oppABCDF 1.35
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
fnr 1.30
fnr
FNR DNA-binding transcriptional dual regulator
sdhCDAB-sucABCD 1.24
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
rpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ 1.21
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
sodA 1.17
sodA
superoxide dismutase (Mn)
mdh 1.09
mdh
malate dehydrogenase
treBC 1.07
treC
treB
trehalose-6-phosphate hydrolase
trehalose PTS permease - TreB subunit
ackA 1.07
ackA
acetate kinase
icd 1.02
icd
isocitrate dehydrogenase
lpd 0.87
lpd
lipoamide dehydrogenase
fumA 0.84
fumA
fumarase A
rpoS 0.81
rpoS
RNA polymerase, sigma S (sigma 38) factor
fumAC 0.77
fumA
fumC
fumarase A
fumarase C
aceEF 0.72
aceF
aceE
pyruvate dehydrogenase, E2 subunit
subunit of E1p component of pyruvate dehydrogenase complex
gatYZABCD 0.69
gatY
gatZ
gatD
gatA
gatB
gatC
tagatose-1,6-bisphosphate aldolase 2 subunit GatY
tagatose-1,6-bisphosphate aldolase 2 subunit GatZ
L-galactitol-1-phosphate 5-dehydrogenase
galactitol PTS permease - GatA subunit
galactitol PTS permease - GatB subunit
galactitol PTS permease - GatC subunit
nuoABCEFGHIJKLMN 0.63
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
uvrA 0.55
uvrA
excision nuclease subunit A
hybOABCDEFG 0.46
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
fadL 0.44
fadL
long-chain fatty acid outer membrane porin; bacteriophage T2 receptor
ndh 0.44
ndh
NADH:quinone oxidoreductase II
fumC 0.41
fumC
fumarase C
hemA-prfA-prmC 0.39
hemA
prfA
prmC
glutamyl-tRNA reductase
peptide chain release factor RF1
protein-(glutamine-N5) methyltransferase
ompW 0.21
ompW
outer membrane protein W
lldPRD 0.13
lldP
lldR
lldD
(R)-lactate / (S)-lactate / glycolate:H+ symporter LldP
LldR transcriptional dual regulator
L-lactate dehydrogenase
aceBAK 0.09
aceK
aceB
aceA
isocitrate dehydrogenase phosphatase / isocitrate dehydrogenase kinase
malate synthase A
isocitrate lyase
rutABCDEFG 0.05
rutC
rutB
rutA
rutG
rutF
rutE
rutD
predicted aminoacrylate peracid reductase
peroxyureidoacrylate / ureidoacrylate amido hydrolase
pyrimidine oxygenase
uracil:H+ symporter RutG
flavin reductase
predicted malonic semialdehyde reductase
predicted aminoacrylate hydrolase
ssb 0.04
ssb
ssDNA-binding protein
gadE 0.04
gadE
GadE DNA-binding transcriptional activator
cadBA 0.03
cadA
cadB
lysine decarboxylase 1
lysine:cadaverine antiporter
acnB 0.02
acnB
bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase

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
0.8 2.3 GO:0006108 malate metabolic process(GO:0006108)
0.6 2.5 GO:0006083 acetate metabolic process(GO:0006083)
0.4 0.9 GO:0006103 2-oxoglutarate metabolic process(GO:0006103)
0.4 1.2 GO:0006801 response to superoxide(GO:0000303) superoxide metabolic process(GO:0006801)
0.4 1.9 GO:0006567 threonine catabolic process(GO:0006567)
0.4 4.6 GO:0006101 tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101)
0.4 1.1 GO:0005993 trehalose catabolic process(GO:0005993)
0.2 1.2 GO:0032074 negative regulation of nuclease activity(GO:0032074) negative regulation of ribonuclease activity(GO:0060701) negative regulation of endoribonuclease activity(GO:0060702)
0.2 1.0 GO:0035672 oligopeptide transport(GO:0006857) oligopeptide transmembrane transport(GO:0035672)
0.2 0.7 GO:0019407 hexitol metabolic process(GO:0006059) hexitol catabolic process(GO:0019407)
0.2 1.3 GO:0000302 response to reactive oxygen species(GO:0000302)
0.2 0.8 GO:0001121 transcription from bacterial-type RNA polymerase promoter(GO:0001121)
0.2 0.5 GO:0019405 alditol catabolic process(GO:0019405) glycerol catabolic process(GO:0019563)
0.1 0.4 GO:0006479 protein methylation(GO:0006479) protein alkylation(GO:0008213)
0.1 1.4 GO:0034599 cellular response to oxidative stress(GO:0034599)
0.1 0.2 GO:1902600 hydrogen ion transmembrane transport(GO:1902600)
0.0 0.4 GO:0006869 lipid transport(GO:0006869)
0.0 0.4 GO:0055076 transition metal ion homeostasis(GO:0055076)
0.0 1.0 GO:0006979 response to oxidative stress(GO:0006979)
0.0 0.1 GO:0007584 response to nutrient(GO:0007584)
0.0 0.7 GO:0006090 pyruvate metabolic process(GO:0006090)
0.0 0.1 GO:0006208 pyrimidine nucleobase catabolic process(GO:0006208) pyrimidine nucleobase transport(GO:0015855)
0.0 0.6 GO:0006281 DNA repair(GO:0006281)
0.0 0.0 GO:0009068 aspartate family amino acid catabolic process(GO:0009068)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.5 4.4 GO:0045239 tricarboxylic acid cycle enzyme complex(GO:0045239) dihydrolipoyl dehydrogenase complex(GO:0045240) oxoglutarate dehydrogenase complex(GO:0045252)
0.2 0.6 GO:0070470 respiratory chain(GO:0070469) plasma membrane respiratory chain(GO:0070470) respiratory chain complex(GO:0098803)
0.1 0.5 GO:0009380 excinuclease repair complex(GO:0009380)
0.1 1.2 GO:0015934 large ribosomal subunit(GO:0015934) cytosolic large ribosomal subunit(GO:0022625)
0.1 1.6 GO:0019898 extrinsic component of membrane(GO:0019898)
0.0 1.0 GO:0043190 ATP-binding cassette (ABC) transporter complex(GO:0043190) ATPase dependent transmembrane transport complex(GO:0098533) ATPase complex(GO:1904949)
0.0 7.2 GO:0005829 cytosol(GO:0005829)
0.0 0.6 GO:0009279 cell outer membrane(GO:0009279)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.5 4.4 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)
0.5 1.4 GO:0005469 succinate:fumarate antiporter activity(GO:0005469)
0.5 1.9 GO:0008861 formate C-acetyltransferase activity(GO:0008861)
0.5 1.4 GO:0051920 peroxiredoxin activity(GO:0051920)
0.5 1.4 GO:0035673 oligopeptide transporter activity(GO:0015198) peptidoglycan transporter activity(GO:0015647) oligopeptide transmembrane transporter activity(GO:0035673)
0.4 2.0 GO:0004333 fumarate hydratase activity(GO:0004333)
0.4 1.2 GO:0004784 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
0.4 1.1 GO:0015927 trehalase activity(GO:0015927)
0.4 1.1 GO:0008137 NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
0.3 1.2 GO:0001072 RNA binding transcription factor activity(GO:0001070) transcription antitermination factor activity, RNA binding(GO:0001072) ribonuclease inhibitor activity(GO:0008428)
0.2 0.7 GO:0031405 lipoic acid binding(GO:0031405)
0.2 0.8 GO:0001000 bacterial-type RNA polymerase core enzyme binding(GO:0001000)
0.1 0.4 GO:0022836 ion channel activity(GO:0005216) gated channel activity(GO:0022836) transmembrane receptor activity(GO:0099600)
0.1 0.9 GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor(GO:0016668)
0.1 1.1 GO:0016774 phosphotransferase activity, carboxyl group as acceptor(GO:0016774)
0.1 0.5 GO:1902670 carbon dioxide binding(GO:1902670)
0.1 0.4 GO:0008276 protein methyltransferase activity(GO:0008276)
0.1 1.0 GO:0051287 NAD binding(GO:0051287)
0.1 0.7 GO:0016832 aldehyde-lyase activity(GO:0016832)
0.0 0.1 GO:0016208 AMP binding(GO:0016208)
0.0 0.1 GO:0005350 monooxygenase activity(GO:0004497) pyrimidine nucleobase transmembrane transporter activity(GO:0005350)
0.0 0.0 GO:0015491 cation:cation antiporter activity(GO:0015491)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 1.2 REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT Genes involved in The citric acid (TCA) cycle and respiratory electron transport