GSE67402: E.coli regulatory changes under long-term starvation
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
cra
|
cra | Cra DNA-binding transcriptional dual regulator |
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| cra | 0.89 | 4.5e-10 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| gapA | 65.64 |
gapA
|
glyceraldehyde 3-phosphate dehydrogenase |
|
| eno | 48.42 |
eno
|
enolase |
|
| gapA-yeaD | 36.22 |
gapA
yeaD
|
glyceraldehyde 3-phosphate dehydrogenase conserved protein |
|
| adhE | 28.51 |
adhE
|
aldehyde-alcohol dehydrogenase |
|
| epd-pgk-fbaA | 26.50 |
epd
pgk
fbaA
|
erythrose 4-phosphate dehydrogenase phosphoglycerate kinase fructose bisphosphate aldolase class II |
|
| acnB | 24.66 |
acnB
|
bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase |
|
| crp | 24.37 |
crp
|
CRP transcriptional dual regulator |
|
| icd | 23.86 |
icd
|
isocitrate dehydrogenase |
|
| ppc | 20.93 |
ppc
|
phosphoenolpyruvate carboxylase |
|
| tpiA | 18.10 |
tpiA
|
triosephosphate isomerase |
|
| pdhR-aceEF-lpd | 16.60 |
pdhR
lpd
aceF
aceE
|
PdhR DNA-binding transcriptional dual regulator lipoamide dehydrogenase pyruvate dehydrogenase, E2 subunit subunit of E1p component of pyruvate dehydrogenase complex |
|
| gpmM-envC-yibQ | 16.48 |
envC
yibQ
gpmM
|
EnvC divisome associated factor, activator of peptidoglycan hydrolases putative nucleoside (IDP) diphosphatase 2,3-bisphosphoglycerate-independent phosphoglycerate mutase |
|
| epd-pgk | 16.32 |
epd
pgk
|
erythrose 4-phosphate dehydrogenase phosphoglycerate kinase |
|
| nirBDC-cysG | 14.71 |
nirD
cysG
nirC
nirB
|
nitrite reductase, small subunit siroheme synthase subunit nitrite transporter NirC nitrite reductase, large subunit |
|
| fruBKA | 11.40 |
fruK
fruB
fruA
|
1-phosphofructokinase fructose PTS permease - FruB subunit fructose PTS permease - FruA subunit |
|
| ptsHI-crr | 11.24 |
ptsI
ptsH
crr
|
PTS enzyme I HPr Enzyme IIAGlc; Crr |
|
| mpl | 11.07 |
mpl
|
UDP-N-acetylmuramate:L-alanyl-γ-D-glutamyl-meso-diaminoheptanedioate-D-alanine ligase/UDP-N-acetylmuramate:L-alanyl-γ-D-glutamyl-meso-diaminopimelate ligase |
|
| pfkA | 10.06 |
pfkA
|
6-phosphofructokinase I |
|
| cyoABCDE | 9.89 |
cyoA
cyoC
cyoB
cyoE
cyoD
|
cytochrome bo terminal oxidase subunit II cytochrome bo terminal oxidase subunit III cytochrome bo terminal oxidase subunit I heme O synthase cytochrome bo terminal oxidase subunit IV |
|
| zwf | 8.32 |
zwf
|
glucose-6-phosphate dehydrogenase (NADP+) |
|
| pykF | 5.97 |
pykF
|
pyruvate kinase I |
|
| edd-eda | 5.71 |
eda
edd
|
multifunctional 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase and oxaloacetate decarboxylase phosphogluconate dehydratase |
|
| manXYZ | 5.23 |
manX
manY
manZ
|
mannose PTS permease - ManX subunit mannose PTS permease - ManY subunit mannose PTS permease - ManZ subunit |
|
| aroP | 4.95 |
aroP
|
aromatic amino acid:H+ symporter AroP |
|
| betIBA | 4.72 |
betB
betI
betA
|
betaine aldehyde dehydrogenase BetI DNA-binding transcriptional repressor choline dehydrogenase |
|
| csgDEFG | 3.35 |
csgG
csgF
csgE
csgD
|
curli secretion channel curli assembly component curli transport specificity factor CsgD DNA-binding transcriptional dual regulator |
|
| cydAB | 0.57 |
cydA
cydB
|
cytochrome bd-I terminal oxidase subunit I cytochrome bd-I terminal oxidase subunit II |
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 13.0 | 220.9 | GO:0006096 | glycolytic process(GO:0006096) |
| 9.5 | 28.5 | GO:0006067 | ethanol metabolic process(GO:0006067) |
| 8.3 | 16.6 | GO:0006103 | 2-oxoglutarate metabolic process(GO:0006103) |
| 6.1 | 24.4 | GO:0007584 | response to nutrient(GO:0007584) |
| 5.6 | 11.2 | GO:0031329 | regulation of glucose metabolic process(GO:0010906) regulation of cellular catabolic process(GO:0031329) regulation of cellular carbohydrate catabolic process(GO:0043471) |
| 5.5 | 16.6 | GO:0015755 | fructose transport(GO:0015755) |
| 5.5 | 16.5 | GO:0000920 | cell separation after cytokinesis(GO:0000920) |
| 5.1 | 15.4 | GO:0019626 | short-chain fatty acid catabolic process(GO:0019626) |
| 4.9 | 14.7 | GO:0015707 | nitrite transport(GO:0015707) |
| 3.3 | 9.9 | GO:0046034 | ATP metabolic process(GO:0046034) |
| 2.8 | 8.3 | GO:0009372 | quorum sensing(GO:0009372) |
| 2.2 | 24.4 | GO:0022900 | electron transport chain(GO:0022900) |
| 1.6 | 4.9 | GO:0015827 | tryptophan transport(GO:0015827) |
| 1.2 | 4.7 | GO:0006577 | amino-acid betaine metabolic process(GO:0006577) |
| 1.1 | 5.7 | GO:0019521 | D-gluconate metabolic process(GO:0019521) D-gluconate catabolic process(GO:0046177) |
| 0.5 | 3.3 | GO:0043900 | regulation of multi-organism process(GO:0043900) regulation of single-species biofilm formation(GO:1900190) |
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 16.1 | 48.4 | GO:0005856 | cytoskeleton(GO:0005856) |
| 3.5 | 10.5 | GO:0070069 | cytochrome complex(GO:0070069) |
| 3.3 | 26.5 | GO:0005618 | cell wall(GO:0005618) |
| 1.7 | 10.1 | GO:0061695 | transferase complex, transferring phosphorus-containing groups(GO:0061695) |
| 1.6 | 16.5 | GO:0032153 | cell division site(GO:0032153) |
| 1.2 | 22.6 | GO:0019897 | extrinsic component of plasma membrane(GO:0019897) |
| 0.8 | 16.6 | GO:1990204 | oxidoreductase complex(GO:1990204) |
| 0.6 | 3.3 | GO:0031246 | periplasmic side of cell outer membrane(GO:0031241) intrinsic component of periplasmic side of cell outer membrane(GO:0031246) |
| 0.5 | 220.5 | GO:0005829 | cytosol(GO:0005829) |
| 0.2 | 14.7 | GO:0043234 | protein complex(GO:0043234) |
| 0.2 | 11.1 | GO:0005737 | cytoplasm(GO:0005737) |
| 0.0 | 1.6 | GO:0005887 | integral component of plasma membrane(GO:0005887) |
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 36.2 | 144.7 | GO:0043891 | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity(GO:0004365) glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity(GO:0043891) |
| 7.2 | 21.5 | GO:0008443 | phosphofructokinase activity(GO:0008443) |
| 4.9 | 14.7 | GO:0015113 | ferrochelatase activity(GO:0004325) nitrite transmembrane transporter activity(GO:0015113) |
| 3.3 | 9.9 | GO:0048039 | ubiquinone binding(GO:0048039) |
| 3.3 | 16.5 | GO:0016868 | intramolecular transferase activity, phosphotransferases(GO:0016868) |
| 2.8 | 16.6 | GO:0031405 | lipoic acid binding(GO:0031405) |
| 2.4 | 33.2 | GO:0016620 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor(GO:0016620) |
| 1.8 | 68.5 | GO:0016836 | hydro-lyase activity(GO:0016836) |
| 1.6 | 4.9 | GO:0015196 | proton motive force dependent protein transmembrane transporter activity(GO:0009977) L-phenylalanine transmembrane transporter activity(GO:0015192) L-tryptophan transmembrane transporter activity(GO:0015196) |
| 1.6 | 11.2 | GO:0008047 | enzyme activator activity(GO:0008047) |
| 1.6 | 23.9 | GO:0051287 | NAD binding(GO:0051287) |
| 1.3 | 18.1 | GO:0016861 | intramolecular oxidoreductase activity, interconverting aldoses and ketoses(GO:0016861) |
| 1.1 | 11.1 | GO:0016881 | acid-amino acid ligase activity(GO:0016881) |
| 0.9 | 16.0 | GO:0016831 | carboxy-lyase activity(GO:0016831) |
| 0.7 | 5.2 | GO:0015149 | hexose transmembrane transporter activity(GO:0015149) |
| 0.2 | 0.6 | GO:0016679 | oxidoreductase activity, acting on diphenols and related substances as donors(GO:0016679) oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor(GO:0016682) |
| 0.2 | 3.3 | GO:0000987 | bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding(GO:0000986) core promoter proximal region sequence-specific DNA binding(GO:0000987) core promoter proximal region DNA binding(GO:0001159) |
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.9 | 5.7 | NABA MATRISOME | Ensemble of genes encoding extracellular matrix and extracellular matrix-associated proteins |
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 6.1 | 24.4 | REACTOME INNATE IMMUNE SYSTEM | Genes involved in Innate Immune System |
| 3.7 | 11.1 | REACTOME PLATELET ACTIVATION SIGNALING AND AGGREGATION | Genes involved in Platelet activation, signaling and aggregation |