GSE67402: E.coli regulatory changes under long-term starvation
Gene Symbol | Gene ID | Gene Info |
---|---|---|
infA
|
infA | integration host factor subunit alpha |
infB
|
infB | integration host factor subunit beta |
Promoter | Log-likelihood | Transcript | Gene | Gene Info |
---|---|---|---|---|
ilvL | 5.92 |
ilvL
|
ilvGEDA operon leader peptide |
|
acs-yjcH-actP | 5.48 |
acs
actP
yjcH
|
acetyl-CoA synthetase (AMP-forming) acetate / glycolate : cation symporter conserved inner membrane protein |
|
uspB | 5.34 |
uspB
|
predicted universal stress (ethanol tolerance) protein B |
|
ilvLXG_1G_2MEDA | 4.35 |
ilvE
ilvX
ilvM
ilvL
ilvG_1
ilvD
ilvG_2
ilvA
|
branched-chain amino-acid aminotransferase small protein acetolactate synthase / acetohydroxybutanoate synthase, regulatory subunit ilvGEDA operon leader peptide acetolactate synthase II, large subunit, N-ter fragment (pseudogene) dihydroxy acid dehydratase acetolactate synthase II, large subunit, C-ter fragment (pseudogene) threonine deaminase |
|
glcDEFGBA | 4.05 |
glcD
glcE
glcF
glcG
glcA
glcB
|
glycolate oxidase, predicted FAD-linked subunit glycolate oxidase, predicted FAD-binding subunit glycolate oxidase, predicted iron-sulfur subunit conserved protein glycolate / lactate:H+ symporter malate synthase G |
|
yadV-htrE | 4.00 |
htrE
yadV
|
putative outer membrane usher protein probable pilin chaperone similar to PapD |
|
patA | 3.85 |
patA
|
putrescine aminotransferase |
|
osmY | 3.44 |
osmY
|
periplasmic chaperone, osmotically induced |
|
ssuEADCB | 3.08 |
ssuE
ssuD
ssuA
ssuC
ssuB
|
NADPH-dependent FMN reductase alkanesulfonate monooxygenase, FMNH2-dependent aliphatic sulfonate ABC transporter - periplasmic binding protein aliphatic sulfonate ABC transporter - membrane subunit aliphatic sulfonate ABC transporter - ATP binding subunit |
|
ihfA | 2.92 |
ihfA
|
integration host factor (IHF), α subunit |
|
ompC | 2.90 |
ompC
|
outer membrane protein C |
|
dps | 2.82 |
dps
|
stationary phase nucleoid protein that sequesters iron and protects DNA from damage |
|
folA | 2.67 |
folA
|
dihydrofolate reductase |
|
aceBAK | 2.61 |
aceK
aceB
aceA
|
isocitrate dehydrogenase phosphatase / isocitrate dehydrogenase kinase malate synthase A isocitrate lyase |
|
narK | 2.47 |
narK
|
nitrate:nitrite antiporter NarK |
|
paaABCDEFGHIJK | 2.15 |
paaB
paaC
paaA
paaF
paaG
paaD
paaE
paaJ
paaK
paaH
paaI
|
ring 1,2-phenylacetyl-CoA epoxidase subunit ring 1,2-phenylacetyl-CoA epoxidase, structural subunit ring 1,2-phenylacetyl-CoA epoxidase, monooxygenase subunit predicted 2,3-dehydroadipyl-CoA hydratase predicted ring 1,2-epoxyphenylacetyl-CoA isomerase (oxepin-CoA forming) phenylacetate degradation protein ring 1,2-phenylacetyl-CoA epoxidase, reductase subunit β-ketoadipyl-CoA thiolase phenylacetate-CoA ligase 3-hydroxyadipyl-CoA dehydrogenase (NAD+) phenylacetyl-CoA thioesterase |
|
narGHJI | 2.01 |
narG
narI
narH
narJ
|
nitrate reductase A, α subunit nitrate reductase A, γ subunit nitrate reductase A, β subunit molybdenum cofactor assembly chaperone subunit (δ subunit) of nitrate reductase 1 |
|
yjbE | 1.96 |
yjbE
|
predicted protein |
|
tyrP | 1.94 |
tyrP
|
tyrosine:H+ symporter TyrP |
|
atoDAEB | 1.80 |
atoB
atoA
atoD
atoE
|
acetyl-CoA acetyltransferase acetyl-CoA:acetoacetyl-CoA transferase, β subunit acetyl-CoA:acetoacetyl-CoA transferase, α subunit predicted short chain fatty acid transporter |
|
pstS | 1.74 |
pstS
|
phosphate ABC transporter - periplasmic binding protein |
|
ibpB | 1.72 |
ibpB
|
small heat shock protein IbpB |
|
fimAICDFGH | 1.72 |
fimA
fimC
fimD
fimF
fimG
fimH
fimI
|
major type 1 subunit fimbrin (pilin) periplasmic chaperone, required for type 1 fimbriae outer membrane protein; export and assembly of type 1 fimbriae fimbrial morphology fimbrial morphology minor fimbrial subunit, D-mannose specific adhesin fimbrial protein |
|
osmE | 1.72 |
osmE
|
osmotically inducible protein OsmE |
|
paaZ | 1.71 |
paaZ
|
oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase |
|
hipBA | 1.71 |
hipA
hipB
|
serine/threonine kinase HipA HipB antitoxin and DNA-binding transcriptional repressor |
|
yjbEFGH | 1.65 |
yjbG
yjbF
yjbE
yjbH
|
conserved protein predicted lipoprotein predicted protein predicted porin |
|
yeiL | 1.64 |
yeiL
|
YeiL DNA-binding transcriptional activator |
|
adiA | 1.57 |
adiA
|
arginine decarboxylase, degradative |
|
sufABCDSE | 1.33 |
sufB
sufC
sufA
sufD
sufE
sufS
|
SufB component of SufBCD Fe-S cluster scaffold complex SufC component of SufBCD Fe-S cluster scaffold complex Fe-S transport protein in Fe-S cluster assembly SufD component of SufBCD Fe-S cluster scaffold complex sulfur acceptor for SufS cysteine desulfurase L-cysteine desulfurase |
|
uspA | 1.31 |
uspA
|
universal stress global stress response regulator |
|
glmY | 1.12 |
glmY
|
GlmY |
|
glpTQ | 1.11 |
glpT
glpQ
|
glycerol-3-phosphate:phosphate antiporter glycerophosphoryl diester phosphodiesterase, periplasmic |
|
ompR-envZ | 1.01 |
envZ
ompR
|
EnvZ OmpR transcriptional dual regulator |
|
yiaKLMNO-lyxK-sgbHUE | 0.95 |
lyxK
sgbH
sgbE
sgbU
yiaK
yiaM
yiaL
yiaO
yiaN
|
L-xylulose kinase 3-keto-L-gulonate 6-phosphate decarboxylase L-ribulose-5-phosphate 4-epimerase predicted L-xylulose 5-phosphate 3-epimerase 2,3-diketo-L-gulonate reductase 2,3-diketo-L-gulonate:Na+ symporter - membrane subunit conserved protein 2,3-diketo-L-gulonate:Na+ symporter - periplasmic binding protein 2,3-diketo-L-gulonate:Na+ symporter - membrane subunit |
|
pstSCA | 0.91 |
pstS
pstC
pstA
|
phosphate ABC transporter - periplasmic binding protein phosphate ABC transporter - membrane subunit phosphate ABC transporter - membrane subunit |
|
mtr | 0.88 |
mtr
|
tryptohan / indole:H+ symporter Mtr |
|
ulaG | 0.85 |
ulaG
|
L-ascorbate 6-phosphate lactonase |
|
dcuD | 0.79 |
dcuD
|
putative transport protein, C4-dicarboxylate uptake C family |
|
ulaABCDEF | 0.75 |
ulaD
ulaE
ulaF
ulaA
ulaB
ulaC
|
3-keto-L-gulonate 6-phosphate decarboxylase L-xylulose 5-phosphate 3-epimerase L-ribulose 5-phosphate 4-epimerase L-ascorbate PTS permease - UlaA subunit L-ascorbate PTS permease - UlaB subunit L-ascorbate PTS permease - UlaC subunit |
|
ubiCA | 0.74 |
ubiC
ubiA
|
chorismate lyase 4-hydroxybenzoate octaprenyltransferase |
|
hemF | 0.51 |
hemF
|
coproporphyrinogen III oxidase |
|
dmsABC | 0.50 |
dmsA
dmsB
dmsC
|
dimethyl sulfoxide reductase, chain A dimethyl sulfoxide reductase, chain B dimethyl sulfoxide reductase, chain C |
|
hycABCDEFGHI | 0.41 |
hycD
hycE
hycF
hycG
hycA
hycB
hycC
hycH
hycI
|
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 |
|
rpoH | 0.22 |
rpoH
|
RNA polymerase, sigma 32 (sigma H) factor |
|
rtcBA | 0.20 |
rtcB
rtcA
|
RNA-splicing ligase RtcB RNA 3'-terminal phosphate cyclase |
|
tdcABCDEFG | 0.10 |
tdcE
tdcD
tdcG
tdcF
tdcA
tdcC
tdcB
|
2-ketobutyrate formate-lyase/pyruvate formate-lyase 4, inactive propionate kinase L-serine deaminase III predicted enamine/imine deaminase TdcA DNA-binding transcriptional activator serine / threonine:H+ symporter TdcC catabolic threonine dehydratase |
|
hypABCDE | 0.06 |
hypE
hypD
hypA
hypC
hypB
|
hydrogenase maturation protein, carbamoyl dehydratase HypD, scaffold protein for assembly of the Fe-(CN)2CO cofactor accessory protein for nickel incorporation into hydrogenase 3 HypC, protein involved in hydrogenase 3 maturation accessory protein for nickel incorporation into hydrogenase isoenzymes |
|
norVW | 0.00 |
norW
norV
|
NADH:flavorubredoxin reductase flavorubredoxin |
Log-likelihood per target | Total log-likelihood | Term | Description |
---|---|---|---|
2.7 | 5.3 | GO:0097305 | response to alcohol(GO:0097305) |
1.8 | 5.5 | GO:0018394 | tellurite transport(GO:0015710) peptidyl-lysine acetylation(GO:0018394) post-translational protein modification(GO:0043687) |
1.5 | 10.3 | GO:0009099 | valine biosynthetic process(GO:0009099) |
1.4 | 5.7 | GO:0043711 | pilus organization(GO:0043711) |
1.3 | 6.7 | GO:0046487 | glyoxylate metabolic process(GO:0046487) |
1.2 | 3.6 | GO:0046379 | extracellular polysaccharide biosynthetic process(GO:0045226) extracellular polysaccharide metabolic process(GO:0046379) |
1.0 | 3.1 | GO:0009970 | cellular response to sulfate starvation(GO:0009970) xenobiotic transport(GO:0042908) |
1.0 | 4.0 | GO:0015748 | organophosphate ester transport(GO:0015748) |
1.0 | 3.9 | GO:0042178 | xenobiotic catabolic process(GO:0042178) |
0.9 | 1.8 | GO:0019626 | short-chain fatty acid catabolic process(GO:0019626) |
0.7 | 2.0 | GO:0071941 | nitrogen cycle metabolic process(GO:0071941) |
0.6 | 3.8 | GO:0009447 | polyamine catabolic process(GO:0006598) putrescine catabolic process(GO:0009447) |
0.5 | 1.6 | GO:0015707 | nitrite transport(GO:0015707) |
0.5 | 2.7 | GO:0046654 | tetrahydrofolate biosynthetic process(GO:0046654) |
0.5 | 1.6 | GO:0006527 | arginine catabolic process(GO:0006527) |
0.5 | 2.5 | GO:0010921 | regulation of phosphatase activity(GO:0010921) |
0.3 | 1.7 | GO:1990169 | stress response to copper ion(GO:1990169) |
0.3 | 1.7 | GO:0018105 | peptidyl-serine phosphorylation(GO:0018105) |
0.3 | 1.0 | GO:0048583 | regulation of response to stimulus(GO:0048583) |
0.3 | 0.9 | GO:0019324 | L-lyxose metabolic process(GO:0019324) |
0.3 | 0.9 | GO:0015827 | tryptophan transport(GO:0015827) |
0.2 | 1.3 | GO:0097428 | protein maturation by iron-sulfur cluster transfer(GO:0097428) |
0.1 | 0.7 | GO:1901661 | ubiquinone metabolic process(GO:0006743) ubiquinone biosynthetic process(GO:0006744) ketone biosynthetic process(GO:0042181) quinone metabolic process(GO:1901661) quinone biosynthetic process(GO:1901663) |
0.1 | 2.9 | GO:0006970 | response to osmotic stress(GO:0006970) |
0.1 | 2.8 | GO:0042594 | response to starvation(GO:0042594) |
0.1 | 0.8 | GO:0006835 | dicarboxylic acid transport(GO:0006835) C4-dicarboxylate transport(GO:0015740) |
0.1 | 0.7 | GO:0051180 | vitamin transport(GO:0051180) |
0.1 | 0.4 | GO:0016485 | protein processing(GO:0016485) |
0.1 | 0.2 | GO:0001121 | transcription from bacterial-type RNA polymerase promoter(GO:0001121) |
0.0 | 0.1 | GO:0046459 | short-chain fatty acid metabolic process(GO:0046459) |
0.0 | 0.2 | GO:0042245 | RNA repair(GO:0042245) |
0.0 | 0.8 | GO:0006766 | vitamin metabolic process(GO:0006766) water-soluble vitamin metabolic process(GO:0006767) |
Log-likelihood per target | Total log-likelihood | Term | Description |
---|---|---|---|
0.7 | 2.0 | GO:0031235 | intrinsic component of the cytoplasmic side of the plasma membrane(GO:0031235) |
0.6 | 4.5 | GO:0045203 | integral component of cell outer membrane(GO:0045203) |
0.2 | 1.7 | GO:0042995 | cell projection(GO:0042995) |
0.2 | 0.5 | GO:0031237 | intrinsic component of periplasmic side of plasma membrane(GO:0031237) |
0.1 | 1.7 | GO:0055052 | ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing(GO:0055052) |
0.0 | 16.8 | GO:0005886 | plasma membrane(GO:0005886) |
Log-likelihood per target | Total log-likelihood | Term | Description |
---|---|---|---|
2.4 | 9.5 | GO:0043879 | glycolate transmembrane transporter activity(GO:0043879) |
1.8 | 1.8 | GO:0003988 | acetyl-CoA C-acyltransferase activity(GO:0003988) |
1.4 | 4.3 | GO:0003984 | acetolactate synthase activity(GO:0003984) |
1.0 | 3.1 | GO:0004497 | monooxygenase activity(GO:0004497) |
0.9 | 2.6 | GO:0046912 | AMP binding(GO:0016208) transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer(GO:0046912) |
0.8 | 3.9 | GO:0004300 | enoyl-CoA hydratase activity(GO:0004300) |
0.6 | 1.7 | GO:0008742 | L-ribulose-phosphate 4-epimerase activity(GO:0008742) |
0.5 | 1.6 | GO:0015113 | nitrite transmembrane transporter activity(GO:0015113) |
0.5 | 2.0 | GO:0008940 | nitrate reductase activity(GO:0008940) metallochaperone activity(GO:0016530) |
0.5 | 2.5 | GO:0042301 | phosphate ion binding(GO:0042301) |
0.4 | 1.7 | GO:0044183 | protein binding involved in protein folding(GO:0044183) |
0.4 | 1.1 | GO:0015166 | polyol transmembrane transporter activity(GO:0015166) |
0.3 | 0.9 | GO:0015196 | L-tryptophan transmembrane transporter activity(GO:0015196) |
0.2 | 3.8 | GO:0008483 | transaminase activity(GO:0008483) |
0.2 | 1.3 | GO:0008047 | enzyme activator activity(GO:0008047) |
0.2 | 0.7 | GO:0004659 | prenyltransferase activity(GO:0004659) |
0.2 | 1.0 | GO:0000156 | phosphorelay response regulator activity(GO:0000156) |
0.1 | 1.7 | GO:0030170 | pyridoxal phosphate binding(GO:0030170) |
0.1 | 0.8 | GO:0052689 | carboxylic ester hydrolase activity(GO:0052689) |
0.1 | 1.7 | GO:0004672 | protein kinase activity(GO:0004672) |
0.1 | 0.4 | GO:0016151 | nickel cation binding(GO:0016151) |
0.0 | 1.8 | GO:0005506 | iron ion binding(GO:0005506) |
0.0 | 0.2 | GO:0000996 | 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) |
Log-likelihood per target | Total log-likelihood | Term | Description |
---|---|---|---|
0.4 | 4.0 | REACTOME METABOLISM OF CARBOHYDRATES | Genes involved in Metabolism of carbohydrates |