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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
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| arcA | 0.68 | 6.4e-02 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| focA-pflB Show fit | 1.97 |
formate channel FocA pyruvate formate-lyase (inactive) |
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| sucAB Show fit | 1.64 |
subunit of E1(0) component of 2-oxoglutarate dehydrogenase dihydrolipoyltranssuccinylase |
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| sucABCD Show fit | 1.53 |
subunit of E1(0) component of 2-oxoglutarate dehydrogenase succinyl-CoA synthetase, β subunit dihydrolipoyltranssuccinylase succinyl-CoA synthetase, α subunit |
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| dcuC Show fit | 1.44 |
dicarboxylate transporter DcuC |
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| tpx Show fit | 1.42 |
lipid hydroperoxide peroxidase |
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| oppABCDF Show fit | 1.35 |
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 |
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| fnr Show fit | 1.30 |
FNR DNA-binding transcriptional dual regulator |
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| sdhCDAB-sucABCD Show fit | 1.24 |
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 |
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| rpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ Show fit | 1.21 |
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 |
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| sodA Show fit | 1.17 |
superoxide dismutase (Mn) |
Network of associatons between targets according to the STRING database.
First level regulatory network of ArcA
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 4.6 | GO:0006101 | tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101) |
| 0.6 | 2.5 | GO:0006083 | acetate metabolic process(GO:0006083) |
| 0.8 | 2.3 | GO:0006108 | malate metabolic process(GO:0006108) |
| 0.4 | 1.9 | GO:0006567 | threonine catabolic process(GO:0006567) |
| 0.1 | 1.4 | GO:0034599 | cellular response to oxidative stress(GO:0034599) |
| 0.2 | 1.3 | GO:0000302 | response to reactive oxygen species(GO:0000302) |
| 0.4 | 1.2 | GO:0006801 | response to superoxide(GO:0000303) superoxide metabolic process(GO:0006801) |
| 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) |
| 0.4 | 1.1 | GO:0005993 | trehalose catabolic process(GO:0005993) |
| 0.2 | 1.0 | GO:0035672 | oligopeptide transport(GO:0006857) oligopeptide transmembrane transport(GO:0035672) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 7.2 | GO:0005829 | cytosol(GO:0005829) |
| 1.5 | 4.4 | GO:0045239 | tricarboxylic acid cycle enzyme complex(GO:0045239) dihydrolipoyl dehydrogenase complex(GO:0045240) oxoglutarate dehydrogenase complex(GO:0045252) |
| 0.1 | 1.6 | GO:0019898 | extrinsic component of membrane(GO:0019898) |
| 0.1 | 1.2 | GO:0015934 | large ribosomal subunit(GO:0015934) cytosolic large ribosomal subunit(GO:0022625) |
| 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) |
| 0.2 | 0.6 | GO:0070470 | respiratory chain(GO:0070469) plasma membrane respiratory chain(GO:0070470) respiratory chain complex(GO:0098803) |
| 0.0 | 0.6 | GO:0009279 | cell outer membrane(GO:0009279) |
| 0.1 | 0.5 | GO:0009380 | excinuclease repair complex(GO:0009380) |
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) |
| 0.4 | 2.0 | GO:0004333 | fumarate hydratase activity(GO:0004333) |
| 0.5 | 1.9 | GO:0008861 | formate C-acetyltransferase activity(GO:0008861) |
| 0.5 | 1.4 | GO:0005469 | succinate:fumarate antiporter activity(GO:0005469) |
| 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 | 1.2 | GO:0004784 | superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721) |
| 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) |
| 0.4 | 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) |
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 |