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GSE55662: Plasticity of transcriptional regulation under antibiotic stress
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Results for Sigma70
Z-value: 3.45
Transcription factors associated with Sigma70
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| rpoD | 0.99 | 1.4e-06 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| focA-pflB Show fit | 10.57 |
formate channel FocA pyruvate formate-lyase (inactive) |
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| tufA Show fit | 9.69 |
elongation factor Tu |
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| pgk Show fit | 9.65 |
phosphoglycerate kinase |
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| uvrB Show fit | 9.58 |
DNA repair; excision nuclease subunit B |
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| mreB Show fit | 8.41 |
dynamic cytoskeletal protein MreB |
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| gapA Show fit | 8.22 |
glyceraldehyde 3-phosphate dehydrogenase |
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| csrA Show fit | 8.17 |
carbon storage regulator; pleiotropic regulatory protein for carbon source metabolism |
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| pgk-fbaA Show fit | 8.17 |
phosphoglycerate kinase fructose bisphosphate aldolase class II |
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| gltX Show fit | 7.97 |
glutamate-tRNA ligase |
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| icd Show fit | 7.64 |
isocitrate dehydrogenase |
Network of associatons between targets according to the STRING database.
First level regulatory network of Sigma70
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 3.2 | 42.2 | GO:0006096 | glycolytic process(GO:0006096) |
| 2.2 | 38.2 | GO:0006418 | tRNA aminoacylation for protein translation(GO:0006418) tRNA aminoacylation(GO:0043039) |
| 3.8 | 22.9 | GO:0019319 | gluconeogenesis(GO:0006094) hexose biosynthetic process(GO:0019319) |
| 3.9 | 19.6 | GO:0051782 | negative regulation of cell division(GO:0051782) |
| 6.1 | 18.2 | GO:0010906 | regulation of glucose metabolic process(GO:0010906) |
| 1.3 | 18.2 | GO:0006633 | fatty acid biosynthetic process(GO:0006633) |
| 3.5 | 17.5 | GO:2000765 | regulation of cytoplasmic translation(GO:2000765) |
| 3.3 | 16.5 | GO:0030490 | maturation of SSU-rRNA(GO:0030490) |
| 1.1 | 16.1 | GO:0010212 | response to ionizing radiation(GO:0010212) |
| 5.1 | 15.2 | GO:0043242 | negative regulation of protein complex disassembly(GO:0043242) negative regulation of DNA-templated transcription, termination(GO:0060567) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.8 | 353.0 | GO:0005829 | cytosol(GO:0005829) |
| 2.9 | 46.7 | GO:0015935 | small ribosomal subunit(GO:0015935) cytosolic small ribosomal subunit(GO:0022627) |
| 1.8 | 16.0 | GO:0044391 | ribosome(GO:0005840) cytosolic ribosome(GO:0022626) intracellular ribonucleoprotein complex(GO:0030529) ribosomal subunit(GO:0044391) ribonucleoprotein complex(GO:1990904) |
| 1.8 | 14.2 | GO:0005618 | cell wall(GO:0005618) |
| 4.5 | 13.4 | GO:0005856 | cytoskeleton(GO:0005856) |
| 2.3 | 11.4 | GO:0009380 | excinuclease repair complex(GO:0009380) |
| 1.0 | 10.1 | GO:0032153 | cell division site(GO:0032153) |
| 1.8 | 9.0 | GO:0046930 | pore complex(GO:0046930) |
| 2.9 | 8.8 | GO:0045273 | respiratory chain complex II(GO:0045273) plasma membrane respiratory chain complex II(GO:0045274) |
| 0.9 | 8.2 | GO:0031234 | extrinsic component of cytoplasmic side of plasma membrane(GO:0031234) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.5 | 42.6 | GO:0016876 | aminoacyl-tRNA ligase activity(GO:0004812) ligase activity, forming carbon-oxygen bonds(GO:0016875) ligase activity, forming aminoacyl-tRNA and related compounds(GO:0016876) |
| 3.3 | 35.8 | GO:0003735 | structural constituent of ribosome(GO:0003735) |
| 0.3 | 30.6 | GO:0042802 | identical protein binding(GO:0042802) |
| 6.0 | 24.1 | GO:0004618 | phosphoglycerate kinase activity(GO:0004618) |
| 2.9 | 20.2 | GO:0003697 | single-stranded DNA binding(GO:0003697) |
| 4.8 | 19.2 | GO:0001072 | RNA binding transcription factor activity(GO:0001070) transcription antitermination factor activity, RNA binding(GO:0001072) |
| 3.5 | 17.5 | GO:0048027 | mRNA 5'-UTR binding(GO:0048027) |
| 3.1 | 15.3 | GO:0016987 | transcription factor activity, core RNA polymerase binding(GO:0000990) core DNA-dependent RNA polymerase binding promoter specificity activity(GO:0000996) sigma factor activity(GO:0016987) |
| 3.2 | 12.9 | GO:0032843 | hydroperoxide reductase activity(GO:0032843) |
| 2.7 | 11.0 | GO:0008861 | formate C-acetyltransferase activity(GO:0008861) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.4 | 4.1 | PID IL12 2PATHWAY | IL12-mediated signaling events |
| 0.5 | 1.4 | PID CMYB PATHWAY | C-MYB transcription factor network |
| 0.4 | 1.3 | NABA MATRISOME ASSOCIATED | Ensemble of genes encoding ECM-associated proteins including ECM-affilaited proteins, ECM regulators and secreted factors |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.5 | 10.1 | REACTOME METABOLISM OF NUCLEOTIDES | Genes involved in Metabolism of nucleotides |
| 3.2 | 9.6 | REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE | Genes involved in SRP-dependent cotranslational protein targeting to membrane |
| 2.0 | 6.0 | REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT | Genes involved in The citric acid (TCA) cycle and respiratory electron transport |
| 0.6 | 5.8 | REACTOME METABOLISM OF CARBOHYDRATES | Genes involved in Metabolism of carbohydrates |
| 1.1 | 3.3 | REACTOME DEVELOPMENTAL BIOLOGY | Genes involved in Developmental Biology |
| 0.4 | 0.4 | REACTOME METABOLISM OF PROTEINS | Genes involved in Metabolism of proteins |