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GSE55662: Plasticity of transcriptional regulation under antibiotic stress
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Results for Sigma54
Z-value: 0.81
Transcription factors associated with Sigma54
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| rpoN | -0.90 | 2.4e-03 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| rtcR Show fit | 4.00 |
RtcR DNA-binding transcriptional activator |
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| dcuD Show fit | 3.49 |
putative transport protein, C4-dicarboxylate uptake C family |
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| nac Show fit | 3.02 |
Nac DNA-binding transcriptional dual regulator |
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| ygfK-ssnA Show fit | 2.79 |
predicted oxidoreductase, Fe-S subunit predicted chlorohydrolase/aminohydrolase |
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| glnK-amtB Show fit | 2.68 |
nitrogen regulatory protein GlnK ammonia / ammonium transporter |
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| zraP Show fit | 2.57 |
zinc responsive, periplasmic protein with chaperone activity |
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| hyfABCDEFGHIJR-focB Show fit | 2.22 |
hydrogenase 4 component J, putative protein processing element hydrogenase 4, small subunit hydrogenase 4, component H hydrogenase 4, component C hydrogenase 4, component B hydrogenase 4, component A hydrogenase 4, large subunit hydrogenase 4, component F hydrogenase 4, component E hydrogenase 4, component D HyfR DNA-binding transcriptional activator FocB formate FNT transporter |
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| hycABCDEFGHI Show fit | 2.20 |
hydrogenase 3, membrane subunit hydrogenase 3, large subunit formate hydrogenlyase complex iron-sulfur protein hydrogenase 3 and formate hydrogenlyase complex, HycG subunit regulator of the transcriptional regulator FhlA hydrogenase 3, Fe-S subunit hydrogenase 3, membrane subunit protein required for maturation of hydrogenase 3 hydrogenase 3 maturation protease |
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| yhdWXYZ Show fit | 2.05 |
putative transport protein, ABC superfamily - periplasmic binding protein putative transport protein, ABC superfamily - membrane component putative transport protein, ABC superfamily - ATP-binding component putative transport protein, ABC superfamily - membrane component |
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| rtcBA Show fit | 1.62 |
RNA-splicing ligase RtcB RNA 3'-terminal phosphate cyclase |
Network of associatons between targets according to the STRING database.
First level regulatory network of Sigma54
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 5.5 | GO:1902680 | positive regulation of transcription, DNA-templated(GO:0045893) positive regulation of RNA metabolic process(GO:0051254) positive regulation of RNA biosynthetic process(GO:1902680) positive regulation of nucleic acid-templated transcription(GO:1903508) |
| 0.5 | 3.4 | GO:0015740 | C4-dicarboxylate transport(GO:0015740) |
| 0.9 | 2.7 | GO:0006808 | regulation of nitrogen utilization(GO:0006808) |
| 0.4 | 2.2 | GO:0016485 | protein processing(GO:0016485) |
| 0.1 | 2.2 | GO:0015718 | monocarboxylic acid transport(GO:0015718) |
| 0.5 | 1.6 | GO:0015846 | polyamine transport(GO:0015846) putrescine transport(GO:0015847) |
| 0.4 | 1.6 | GO:0042245 | RNA repair(GO:0042245) |
| 0.4 | 1.3 | GO:0046100 | purine nucleobase catabolic process(GO:0006145) hypoxanthine metabolic process(GO:0046100) |
| 0.3 | 1.3 | GO:0043171 | peptide catabolic process(GO:0043171) |
| 0.1 | 0.9 | GO:0006855 | drug transmembrane transport(GO:0006855) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 10.5 | GO:0005887 | integral component of plasma membrane(GO:0005887) |
| 0.1 | 2.2 | GO:1990204 | oxidoreductase complex(GO:1990204) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 7.9 | GO:0003700 | transcription factor activity, sequence-specific DNA binding(GO:0003700) |
| 0.4 | 3.3 | GO:0008519 | ammonium transmembrane transporter activity(GO:0008519) |
| 0.0 | 2.8 | GO:0016491 | oxidoreductase activity(GO:0016491) |
| 0.9 | 2.6 | GO:0050897 | cobalt ion binding(GO:0050897) |
| 0.7 | 2.2 | GO:0008137 | NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136) |
| 0.1 | 2.2 | GO:0004175 | endopeptidase activity(GO:0004175) |
| 0.1 | 1.6 | GO:0030145 | manganese ion binding(GO:0030145) |
| 0.5 | 1.4 | GO:0008410 | CoA-transferase activity(GO:0008410) |
| 0.3 | 1.3 | GO:0016755 | transferase activity, transferring amino-acyl groups(GO:0016755) |
| 0.3 | 1.3 | GO:0016725 | oxidoreductase activity, acting on CH or CH2 groups(GO:0016725) |