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GSE67402: E.coli regulatory changes under long-term starvation

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Results for Cra

Z-value: 2.87

Transcription factors associated with Cra

Gene Symbol Gene ID Gene Info
cra
cra Cra DNA-binding transcriptional dual regulator

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
cra0.894.5e-10Click!

Activity profile of Cra motif

Sorted Z-values of Cra motif

Top targets:  

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

Network of associatons between targets according to the STRING database.

First level regulatory network of Cra

PNG image of the network

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

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)

Gene overrepresentation in cellular component category:

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)

Gene overrepresentation in molecular function category:

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)

Gene overrepresentation in curated gene sets: canonical pathways category:

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

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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