GSE67402: E.coli regulatory changes under long-term starvation
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
rpoE
|
rpoE | RNA polymerase sigma factor RpoE |
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| rpoE | 0.92 | 2.1e-11 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| yraP | 42.96 |
yraP
|
lipoprotein |
|
| fusA-tufA | 35.77 |
tufA
fusA
|
elongation factor Tu elongation factor G |
|
| bamA-skp-lpxD-fabZ-lpxAB-rnhB-dnaE | 22.99 |
skp
rnhB
lpxA
lpxB
lpxD
bamA
fabZ
dnaE
|
periplasmic chaperone RNAse HII, degrades RNA of DNA-RNA hybrids UDP-N-acetylglucosamine acyltransferase lipid A disaccharide synthase UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase Outer Membrane Protein Assembly Complex - BamA subunit 3-hydroxy-acyl-[acyl-carrier-protein] dehydratase DNA polymerase III, α subunit |
|
| bamD | 22.94 |
bamD
|
Outer Membrane Protein Assembly Complex - BamD subunit |
|
| malQ | 20.83 |
malQ
|
amylomaltase/amylomaltase/amylomaltase |
|
| ybaB-recR | 19.32 |
ybaB
recR
|
conserved DNA-binding protein recombination and repair |
|
| bamA | 19.15 |
bamA
|
Outer Membrane Protein Assembly Complex - BamA subunit |
|
| fkpA | 19.04 |
fkpA
|
peptidyl-prolyl cis-trans isomerase; in protein folding |
|
| bamB-der | 17.73 |
der
bamB
|
50S ribosomal subunit stability factor Outer Membrane Protein Assembly Complex - BamB subunit |
|
| skp-lpxD-fabZ-lpxA | 17.64 |
lpxA
lpxD
skp
fabZ
|
UDP-N-acetylglucosamine acyltransferase UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase periplasmic chaperone 3-hydroxy-acyl-[acyl-carrier-protein] dehydratase |
|
| lptB-rpoN-hpf-ptsN-rapZ | 17.30 |
rapZ
ptsN
rpoN
lptB
hpf
|
RNase adaptor protein phosphotransferase system enzyme IIA, regulation of potassium transport RNA polymerase, sigma 54 (sigma N) factor LptB hibernation promoting factor |
|
| bamC | 16.66 |
bamC
|
Outer Membrane Protein Assembly Complex - BamC subunit |
|
| lptD-surA-pdxA | 16.33 |
lptD
pdxA
surA
|
outer membrane lipopolysaccharide transport and assembly complex - LptD subunit 4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent peptidyl-prolyl cis-trans isomerase (PPIase) |
|
| degP | 15.98 |
degP
|
serine protease Do |
|
| lpxD | 15.47 |
lpxD
|
UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase |
|
| surA-pdxA-rsmA-apaGH | 15.06 |
apaG
pdxA
rsmA
apaH
surA
|
hypothetical protein 4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent 16S rRNA m62A1518,m62A1519 dimethyltransferase diadenosine tetraphosphatase peptidyl-prolyl cis-trans isomerase (PPIase) |
|
| rseP | 14.28 |
rseP
|
intramembrane zinc metalloprotease, signal peptide peptidase |
|
| greA | 13.22 |
greA
|
transcription elongation factor GreA |
|
| lpxP | 12.79 |
lpxP
|
palmitoleoyl acyltransferase |
|
| ygiM-cca | 10.62 |
cca
ygiM
|
fused tRNA nucleotidyltransferase / 2',3'-cyclic phosphodiesterase / 2' nucleotidase and phosphatase predicted signal transduction protein (SH3 domain) |
|
| psd-mscM | 10.01 |
mscM
psd
|
mechanosensitive channel of miniconductance MscM phosphatidylserine decarboxylase, proenzyme |
|
| bepA-yfgD | 9.94 |
yfgD
bepA
|
predicted oxidoreductase chaperone/protease involved in the maintenance of OM integrity |
|
| yfeYX | 9.87 |
yfeX
yfeY
|
porphyrinogen peroxidase predicted outer membrane lipoprotein |
|
| rfaD-waaFCL | 9.84 |
waaC
waaF
waaL
rfaD
|
ADP-heptose:LPS heptosyltransferase I ADP-heptose:LPS heptosyltransferase II O-antigen ligase ADP-L-glycero-D-mannoheptose-6-epimerase |
|
| dsbC-recJ-prfB | 9.55 |
recJ
dsbC
prfB
|
ssDNA-specific exonuclease RecJ protein disulfide isomerase/protein disulfide oxidoreductase - DsbCreduced peptide chain release factor RF2 |
|
| bacA | 9.42 |
bacA
|
undecaprenyl pyrophosphate phosphatase |
|
| yfeKS | 8.80 |
yfeK
yfeS
|
predicted protein conserved protein |
|
| sbmA-yaiW | 8.21 |
sbmA
yaiW
|
peptide antibiotic / peptide nucleic acid transporter surface exposed outer membrane lipoprotein |
|
| clpX-lon | 8.10 |
clpX
lon
|
ClpX DNA-binding, ATP-dependent protease La |
|
| lptAB | 8.09 |
lptA
lptB
|
LptA LptB |
|
| phoQ | 6.40 |
phoQ
|
PhoQ sensory histidine kinase |
|
| ahpF | 5.97 |
ahpF
|
alkyl hydroperoxide reductase, AhpF component |
|
| ygiM | 5.86 |
ygiM
|
predicted signal transduction protein (SH3 domain) |
|
| plsB | 5.73 |
plsB
|
glycerol-3-phosphate acyltransferase |
|
| ibaG | 4.96 |
ibaG
|
predicted DNA-binding transcriptional regulator |
|
| yhjJ | 4.91 |
yhjJ
|
predicted zinc-dependent peptidase |
|
| yieEF | 4.86 |
yieE
yieF
|
predicted phosphopantetheinyl transferase chromate reductase |
|
| yqjA-mzrA | 2.86 |
yqjA
mzrA
|
membrane transport protein; required for proton-motive force (PMF) dependent drug efflux MzrA |
|
| rseABC | 2.73 |
rseB
rseC
rseA
|
rseB protein RseC anti-sigma factor |
|
| yggN | 1.51 |
yggN
|
predicted protein |
|
| rpoH | 1.17 |
rpoH
|
RNA polymerase, sigma 32 (sigma H) factor |
|
| eptB | 0.60 |
eptB
|
Kdo2-lipid A phosphoethanolamine 7''-transferase |
|
| micL | 0.25 |
micL
|
MicL-S small regulatory RNA |
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 14.3 | 100.4 | GO:0051205 | protein insertion into membrane(GO:0051205) |
| 9.6 | 48.0 | GO:0043165 | cell envelope organization(GO:0043163) Gram-negative-bacterium-type cell outer membrane assembly(GO:0043165) membrane biogenesis(GO:0044091) membrane assembly(GO:0071709) |
| 6.3 | 19.0 | GO:0042026 | protein refolding(GO:0042026) |
| 6.3 | 25.4 | GO:0015920 | lipopolysaccharide transport(GO:0015920) |
| 5.0 | 10.0 | GO:0071470 | cellular response to osmotic stress(GO:0071470) |
| 4.8 | 24.1 | GO:0006515 | misfolded or incompletely synthesized protein catabolic process(GO:0006515) |
| 3.9 | 19.3 | GO:0071897 | DNA synthesis involved in DNA repair(GO:0000731) DNA biosynthetic process(GO:0071897) |
| 3.5 | 10.6 | GO:0031123 | RNA 3'-end processing(GO:0031123) |
| 3.5 | 10.4 | GO:0009244 | lipopolysaccharide core region biosynthetic process(GO:0009244) lipopolysaccharide core region metabolic process(GO:0046401) |
| 2.8 | 28.3 | GO:0006643 | membrane lipid metabolic process(GO:0006643) glycolipid metabolic process(GO:0006664) glycolipid biosynthetic process(GO:0009247) membrane lipid biosynthetic process(GO:0046467) lipooligosaccharide metabolic process(GO:1901269) lipooligosaccharide biosynthetic process(GO:1901271) |
| 2.7 | 8.2 | GO:0042884 | microcin transport(GO:0042884) |
| 2.6 | 20.8 | GO:0046352 | disaccharide catabolic process(GO:0046352) |
| 2.4 | 9.6 | GO:0043624 | translational termination(GO:0006415) cellular protein complex disassembly(GO:0043624) |
| 2.1 | 6.4 | GO:0010350 | cellular response to magnesium starvation(GO:0010350) |
| 0.7 | 9.9 | GO:0061077 | chaperone-mediated protein folding(GO:0061077) |
| 0.6 | 5.7 | GO:0008654 | phospholipid metabolic process(GO:0006644) phospholipid biosynthetic process(GO:0008654) |
| 0.6 | 4.9 | GO:0071466 | xenobiotic metabolic process(GO:0006805) response to xenobiotic stimulus(GO:0009410) cellular response to xenobiotic stimulus(GO:0071466) |
| 0.6 | 9.4 | GO:0000270 | peptidoglycan metabolic process(GO:0000270) aminoglycan metabolic process(GO:0006022) glycosaminoglycan metabolic process(GO:0030203) |
| 0.4 | 2.9 | GO:0031399 | regulation of protein modification process(GO:0031399) |
| 0.3 | 1.2 | GO:0001121 | transcription from bacterial-type RNA polymerase promoter(GO:0001121) |
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 14.2 | 99.4 | GO:1990063 | Bam protein complex(GO:1990063) |
| 1.1 | 17.3 | GO:0022627 | small ribosomal subunit(GO:0015935) cytosolic small ribosomal subunit(GO:0022627) |
| 1.0 | 100.9 | GO:0030288 | outer membrane-bounded periplasmic space(GO:0030288) |
| 0.3 | 139.4 | GO:0005829 | cytosol(GO:0005829) |
| 0.2 | 22.0 | GO:0005887 | integral component of plasma membrane(GO:0005887) |
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 13.5 | 40.6 | GO:0008693 | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity(GO:0008693) 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity(GO:0019171) 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity(GO:0047451) |
| 7.8 | 31.4 | GO:0050570 | 4-hydroxythreonine-4-phosphate dehydrogenase activity(GO:0050570) |
| 6.9 | 20.8 | GO:0004133 | glycogen debranching enzyme activity(GO:0004133) |
| 6.3 | 25.4 | GO:0032403 | lipopolysaccharide transmembrane transporter activity(GO:0015221) lipopolysaccharide-transporting ATPase activity(GO:0015437) protein complex binding(GO:0032403) |
| 5.7 | 17.0 | GO:0045152 | antisigma factor binding(GO:0045152) |
| 4.4 | 13.2 | GO:0001108 | basal transcription machinery binding(GO:0001098) bacterial-type RNA polymerase holo enzyme binding(GO:0001108) |
| 3.5 | 17.7 | GO:0097216 | guanosine tetraphosphate binding(GO:0097216) |
| 3.5 | 10.6 | GO:0070567 | cytidylyltransferase activity(GO:0070567) |
| 3.4 | 24.1 | GO:0004252 | serine-type endopeptidase activity(GO:0004252) |
| 3.3 | 10.0 | GO:0022836 | gated channel activity(GO:0022836) |
| 3.2 | 9.6 | GO:0008297 | single-stranded DNA exodeoxyribonuclease activity(GO:0008297) 5'-3' exonuclease activity(GO:0008409) |
| 3.1 | 9.4 | GO:0050380 | undecaprenyl-diphosphatase activity(GO:0050380) |
| 2.7 | 8.2 | GO:0019534 | toxin transporter activity(GO:0019534) |
| 2.5 | 9.9 | GO:0020037 | heme binding(GO:0020037) |
| 2.4 | 4.9 | GO:0008897 | holo-[acyl-carrier-protein] synthase activity(GO:0008897) |
| 2.0 | 6.0 | GO:0070402 | NADPH binding(GO:0070402) |
| 1.7 | 15.5 | GO:0016410 | N-acyltransferase activity(GO:0016410) |
| 1.4 | 9.8 | GO:0050661 | NADP binding(GO:0050661) |
| 1.0 | 5.7 | GO:0008374 | O-acyltransferase activity(GO:0008374) |
| 0.9 | 9.9 | GO:0008237 | metallopeptidase activity(GO:0008237) |
| 0.6 | 12.8 | GO:0016747 | transferase activity, transferring acyl groups other than amino-acyl groups(GO:0016747) |
| 0.3 | 6.4 | GO:0000155 | phosphorelay sensor kinase activity(GO:0000155) protein histidine kinase activity(GO:0004673) |
| 0.3 | 0.6 | GO:0016780 | phosphotransferase activity, for other substituted phosphate groups(GO:0016780) |
| 0.3 | 19.3 | GO:0003677 | DNA binding(GO:0003677) |
| 0.3 | 2.9 | GO:0019899 | enzyme binding(GO:0019899) |
| 0.2 | 67.2 | GO:0005515 | protein binding(GO:0005515) |