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GSE67402: E.coli regulatory changes under long-term starvation
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Results for Sigma54
Z-value: 2.64
Transcription factors associated with Sigma54
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| rpoN | -0.96 | 5.9e-15 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| yeaGH Show fit | 31.88 |
protein kinase conserved protein |
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| gltI-sroC-gltJKL Show fit | 27.45 |
SroC glutamate / aspartate ABC transporter - periplasmic binding protein glutamate / aspartate ABC transporter - membrane subunit glutamate / aspartate ABC transporter - membrane subunit glutamate / aspartate ABC transporter - ATP binding subunit |
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| glmY Show fit | 21.90 |
GlmY |
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| astCADBE Show fit | 21.35 |
arginine succinyltransferase succinylarginine dihydrolase succinylornithine transaminase aldehyde dehydrogenase succinylglutamate desuccinylase |
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| ibpB Show fit | 19.83 |
small heat shock protein IbpB |
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| nac Show fit | 19.76 |
Nac DNA-binding transcriptional dual regulator |
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| prpBCDE Show fit | 19.42 |
2-methylcitrate dehydratase propionyl-CoA synthetase 2-methylisocitrate lyase 2-methylcitrate synthase |
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| zraP Show fit | 19.26 |
zinc responsive, periplasmic protein with chaperone activity |
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| rhaD Show fit | 18.76 |
rhamnulose-1-phosphate aldolase |
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| yaaU Show fit | 18.53 |
putative transport protein YaaU, major facilitator superfamily (MFS) |
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 |
|---|---|---|---|
| 7.3 | 43.6 | GO:0015740 | dicarboxylic acid transport(GO:0006835) C4-dicarboxylate transport(GO:0015740) |
| 10.2 | 30.6 | GO:0019626 | short-chain fatty acid catabolic process(GO:0019626) |
| 0.5 | 25.7 | 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) |
| 5.5 | 22.1 | GO:0051707 | response to biotic stimulus(GO:0009607) response to virus(GO:0009615) response to external biotic stimulus(GO:0043207) response to other organism(GO:0051707) |
| 7.1 | 21.3 | GO:0006527 | succinate metabolic process(GO:0006105) arginine catabolic process(GO:0006527) |
| 1.1 | 20.5 | GO:0051604 | protein maturation(GO:0051604) |
| 4.0 | 19.8 | GO:1990169 | stress response to copper ion(GO:1990169) |
| 4.7 | 18.8 | GO:0019301 | rhamnose metabolic process(GO:0019299) rhamnose catabolic process(GO:0019301) |
| 0.4 | 18.5 | GO:0006979 | response to oxidative stress(GO:0006979) |
| 0.8 | 17.3 | GO:0009267 | cellular response to starvation(GO:0009267) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 99.9 | GO:0005886 | plasma membrane(GO:0005886) |
| 0.4 | 19.3 | GO:0030288 | outer membrane-bounded periplasmic space(GO:0030288) |
| 0.8 | 9.4 | GO:0031234 | extrinsic component of cytoplasmic side of plasma membrane(GO:0031234) |
| 0.4 | 4.8 | GO:0055052 | ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing(GO:0055052) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.6 | 39.8 | GO:0003700 | transcription factor activity, sequence-specific DNA binding(GO:0003700) |
| 5.3 | 21.3 | GO:0016813 | N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity(GO:0003992) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines(GO:0016813) |
| 0.7 | 19.5 | GO:0005506 | iron ion binding(GO:0005506) |
| 4.9 | 19.4 | GO:0046912 | transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer(GO:0046912) |
| 6.4 | 19.3 | GO:0050897 | cobalt ion binding(GO:0050897) |
| 1.0 | 18.8 | GO:0016832 | aldehyde-lyase activity(GO:0016832) |
| 0.7 | 17.2 | GO:0004672 | protein kinase activity(GO:0004672) |
| 5.7 | 17.1 | GO:0016743 | carboxyl- or carbamoyltransferase activity(GO:0016743) |
| 0.9 | 12.9 | GO:0016597 | amino acid binding(GO:0016597) |
| 4.2 | 12.5 | GO:0015654 | tellurite transmembrane transporter activity(GO:0015118) tellurite uptake transmembrane transporter activity(GO:0015654) glycolate transmembrane transporter activity(GO:0043879) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 1.2 | PID ANGIOPOIETIN RECEPTOR PATHWAY | Angiopoietin receptor Tie2-mediated signaling |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 1.2 | REACTOME DEVELOPMENTAL BIOLOGY | Genes involved in Developmental Biology |