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GSE80451: E.coli grown aerobically and anaerobically

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Results for ArcA

Z-value: 0.73

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
arcA-0.828.6e-02Click!

Activity profile of ArcA motif

Sorted Z-values of ArcA motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
sucAB 1.49
sucA
sucB
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
dihydrolipoyltranssuccinylase
glpABC 1.46
glpA
glpC
glpB
anaerobic glycerol-3-phosphate dehydrogenase subunit A
anaerobic glycerol-3-phosphate dehydrogenase subunit C
anaerobic glycerol-3-phosphate dehydrogenase subunit B
ompW 1.40
ompW
outer membrane protein W
dctA 1.38
dctA
C4 dicarboxylate / orotate:H+ symporter
sucABCD 1.35
sucA
sucC
sucB
sucD
subunit of E1(0) component of 2-oxoglutarate dehydrogenase
succinyl-CoA synthetase, β subunit
dihydrolipoyltranssuccinylase
succinyl-CoA synthetase, α subunit
aceBAK 1.34
aceK
aceB
aceA
isocitrate dehydrogenase phosphatase / isocitrate dehydrogenase kinase
malate synthase A
isocitrate lyase
acnB 1.15
acnB
bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase
cydDC 1.14
cydC
cydD
glutathione / L-cysteine exporter - CydC subunit
glutathione / L-cysteine exporter - CydD subunit
puuAP 1.07
puuP
puuA
putrescine:H+ symporter PuuP
glutamate-putrescine ligase
sdhCDAB-sucABCD 0.91
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
icd 0.86
icd
isocitrate dehydrogenase
cyoABCDE 0.78
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
hemA-prfA-prmC 0.73
hemA
prfA
prmC
glutamyl-tRNA reductase
peptide chain release factor RF1
protein-(glutamine-N5) methyltransferase
hybOABCDEFG 0.63
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
treBC 0.50
treC
treB
trehalose-6-phosphate hydrolase
trehalose PTS permease - TreB subunit
ydeA 0.42
ydeA
arabinose exporter
gltA 0.40
gltA
citrate synthase
xylR 0.38
xylR
XylR transcriptional dual regulator
fumA 0.36
fumA
fumarase A
mdh 0.34
mdh
malate dehydrogenase
lldPRD 0.34
lldP
lldR
lldD
(R)-lactate / (S)-lactate / glycolate:H+ symporter LldP
LldR transcriptional dual regulator
L-lactate dehydrogenase
uvrA 0.33
uvrA
excision nuclease subunit A
grcA 0.30
grcA
stress-induced alternate pyruvate formate-lyase subunit
lpd 0.27
lpd
lipoamide dehydrogenase
iraM 0.27
iraM
inhibitor of σS proteolysis
rpoS 0.26
rpoS
RNA polymerase, sigma S (sigma 38) factor
puuDRCBE 0.25
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
dpiBA 0.25
dpiB
dpiA
DpiB sensory histidine kinase
DpiA transcriptional dual regulator
aceEF 0.24
aceF
aceE
pyruvate dehydrogenase, E2 subunit
subunit of E1p component of pyruvate dehydrogenase complex
gadAX 0.24
gadX
gadA
GadX DNA-binding transcriptional dual regulator
glutamate decarboxylase A subunit
aldA 0.22
aldA
aldehyde dehydrogenase A
appCBXA 0.22
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
hyaABCDEF 0.22
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
fadH 0.21
fadH
2,4-dienoyl-CoA reductase
dcuC 0.15
dcuC
dicarboxylate transporter DcuC
rpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ 0.14
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
ubiCA 0.13
ubiC
ubiA
chorismate lyase
4-hydroxybenzoate octaprenyltransferase
gadE 0.09
gadE
GadE DNA-binding transcriptional activator
ybdN 0.09
ybdN
conserved protein
cadBA 0.00
cadA
cadB
lysine decarboxylase 1
lysine:cadaverine antiporter

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
0.7 2.0 GO:0006097 glyoxylate cycle(GO:0006097)
0.4 1.1 GO:0015846 polyamine transport(GO:0015846) putrescine transport(GO:0015847)
0.3 1.5 GO:0015740 dicarboxylic acid transport(GO:0006835) C4-dicarboxylate transport(GO:0015740)
0.3 1.1 GO:0000101 sulfur amino acid transport(GO:0000101)
0.3 3.3 GO:0006101 tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101)
0.2 0.7 GO:0006479 protein methylation(GO:0006479) protein alkylation(GO:0008213)
0.2 0.6 GO:0019563 glycerol catabolic process(GO:0019563)
0.2 0.5 GO:0005993 trehalose catabolic process(GO:0005993)
0.1 0.6 GO:0006004 fucose metabolic process(GO:0006004) fucose catabolic process(GO:0019317) L-fucose metabolic process(GO:0042354) L-fucose catabolic process(GO:0042355)
0.1 0.5 GO:1902600 hydrogen ion transmembrane transport(GO:1902600)
0.1 1.4 GO:0046434 organophosphate catabolic process(GO:0046434)
0.1 0.3 GO:0006103 2-oxoglutarate metabolic process(GO:0006103) glycine decarboxylation via glycine cleavage system(GO:0019464)
0.1 0.3 GO:0010350 negative regulation of catabolic process(GO:0009895) cellular response to magnesium starvation(GO:0010350) regulation of protein catabolic process(GO:0042176) negative regulation of protein catabolic process(GO:0042177)
0.1 0.3 GO:0001121 transcription from bacterial-type RNA polymerase promoter(GO:0001121)
0.1 0.2 GO:0071310 cellular response to organic substance(GO:0071310)
0.1 0.2 GO:0006113 fermentation(GO:0006113)
0.1 0.3 GO:0006598 polyamine catabolic process(GO:0006598) putrescine catabolic process(GO:0009447)
0.1 0.2 GO:0051454 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)
0.0 0.1 GO:0060702 negative regulation of nuclease activity(GO:0032074) negative regulation of ribonuclease activity(GO:0060701) negative regulation of endoribonuclease activity(GO:0060702)
0.0 0.1 GO:1901663 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)
0.0 0.2 GO:0006090 pyruvate metabolic process(GO:0006090)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.2 3.7 GO:0045239 tricarboxylic acid cycle enzyme complex(GO:0045239) dihydrolipoyl dehydrogenase complex(GO:0045240) oxoglutarate dehydrogenase complex(GO:0045252)
0.1 0.8 GO:0098567 periplasmic side of plasma membrane(GO:0098567)
0.1 1.3 GO:1990204 oxidoreductase complex(GO:1990204)
0.1 0.3 GO:0009380 excinuclease repair complex(GO:0009380)
0.0 0.3 GO:0019898 extrinsic component of membrane(GO:0019898)
0.0 1.2 GO:0044462 external encapsulating structure part(GO:0044462)
0.0 0.9 GO:1904949 ATP-binding cassette (ABC) transporter complex(GO:0043190) ATPase dependent transmembrane transport complex(GO:0098533) ATPase complex(GO:1904949)
0.0 0.1 GO:0015934 large ribosomal subunit(GO:0015934) cytosolic large ribosomal subunit(GO:0022625)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.2 3.7 GO:0016624 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)
0.4 1.3 GO:0016208 AMP binding(GO:0016208)
0.4 1.2 GO:0016901 oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor(GO:0016901)
0.3 1.5 GO:0015141 dicarboxylic acid transmembrane transporter activity(GO:0005310) fumarate transmembrane transporter activity(GO:0015138) succinate transmembrane transporter activity(GO:0015141) C4-dicarboxylate transmembrane transporter activity(GO:0015556)
0.3 0.5 GO:0048039 ubiquinone binding(GO:0048039)
0.2 1.1 GO:0016880 acid-ammonia (or amide) ligase activity(GO:0016880)
0.2 0.5 GO:0015927 trehalase activity(GO:0015927)
0.1 0.7 GO:0008276 protein methyltransferase activity(GO:0008276)
0.1 0.8 GO:0005319 lipid transporter activity(GO:0005319)
0.1 0.3 GO:0003867 4-aminobutyrate transaminase activity(GO:0003867)
0.1 0.6 GO:1902670 carbon dioxide binding(GO:1902670)
0.1 0.2 GO:0031405 lipoic acid binding(GO:0031405)
0.1 0.2 GO:0004777 succinate-semialdehyde dehydrogenase (NAD+) activity(GO:0004777)
0.1 0.2 GO:0050308 sugar-phosphatase activity(GO:0050308)
0.1 0.2 GO:0005048 signal sequence binding(GO:0005048)
0.1 0.3 GO:0043856 anti-sigma factor antagonist activity(GO:0043856)
0.1 0.3 GO:0001000 bacterial-type RNA polymerase core enzyme binding(GO:0001000)
0.0 0.1 GO:0008428 ribonuclease inhibitor activity(GO:0008428)
0.0 0.3 GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor(GO:0016668)
0.0 0.1 GO:0004659 prenyltransferase activity(GO:0004659)
0.0 0.9 GO:0051287 NAD binding(GO:0051287)
0.0 0.2 GO:0000156 phosphorelay response regulator activity(GO:0000156)
0.0 0.6 GO:0003729 mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.0 0.2 GO:0001140 transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding(GO:0001140) bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding(GO:0001216)
0.0 0.2 GO:0071949 FAD binding(GO:0071949)
0.0 0.2 GO:0010181 FMN binding(GO:0010181)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.3 0.9 REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT Genes involved in The citric acid (TCA) cycle and respiratory electron transport