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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for CRP

Z-value: 0.92

Transcription factors associated with CRP

Gene Symbol Gene ID Gene Info
crp CRP transcriptional dual regulator

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
crp0.196.5e-01Click!

Activity profile of CRP motif

Sorted Z-values of CRP motif

Promoter Log-likelihood Transcript Gene Gene Info
fur 4.30 Fur transcriptional dual regulator
sodB 1.50 superoxide dismutase (Fe)
preTA 1.41 NADH-dependent dihydropyrimidine dehydrogenase subunit
NADH-dependent dihydropyrimidine dehydrogenase subunit
ompF 1.17 outer membrane porin F
pck 1.01 phosphoenolpyruvate carboxykinase (ATP)
raiA 0.95 stationary phase translation inhibitor and ribosome stability factor
mdh 0.82 malate dehydrogenase
glgS 0.82 surface composition regulator
ompW 0.81 outer membrane protein W
ompA 0.79 outer membrane porin A
aspA 0.74 aspartate ammonia-lyase
manXYZ 0.72 mannose PTS permease - ManX subunit
mannose PTS permease - ManY subunit
mannose PTS permease - ManZ subunit
gatYZABCD 0.71 tagatose-1,6-bisphosphate aldolase 2 subunit GatY
tagatose-1,6-bisphosphate aldolase 2 subunit GatZ
L-galactitol-1-phosphate 5-dehydrogenase
galactitol PTS permease - GatA subunit
galactitol PTS permease - GatB subunit
galactitol PTS permease - GatC subunit
dcuB-fumB 0.68 fumarase B
dicarboxylate transporter DcuB
tnaCAB 0.68 tryptophanase
tryptophanase operon leader peptide
tryptophan:H+ symporter TnaB
ansB 0.68 asparaginase II
ychH 0.61 stress-induced protein
ptsHI-crr 0.61 PTS enzyme I
HPr
Enzyme IIAGlc; Crr
tdcABCDEFG 0.61 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
treBC 0.60 trehalose-6-phosphate hydrolase
trehalose PTS permease - TreB subunit
nupG 0.59 nucleoside:H+ symporter NupG
cyaR 0.57 CyaR
aspA-dcuA 0.54 aspartate ammonia-lyase
dicarboxylate transporter DcuA
lpd 0.51 lipoamide dehydrogenase
nmpC 0.51 outer membrane porin protein; locus of qsr prophage
hupA 0.48 transcriptional dual regulator HU-α (HU-2)
nagE 0.42 N-acetylglucosamine PTS permease
gapA 0.42 glyceraldehyde 3-phosphate dehydrogenase
cspE 0.41 transcription antiterminator and regulator of RNA stability
cspD 0.40 DNA replication inhibitor
rhaSR 0.40 RhaS transcriptional activator
RhaR transcriptional activator
grcA 0.39 stress-induced alternate pyruvate formate-lyase subunit
glgCAP 0.36 glycogen phosphorylase
glycogen synthase
glucose-1-phosphate adenylyltransferase
sdhCDAB-sucABCD 0.35 subunit of E1(0) component of 2-oxoglutarate dehydrogenase
succinyl-CoA synthetase, β subunit
dihydrolipoyltranssuccinylase
succinyl-CoA synthetase, α subunit
succinate:quinone oxidoreductase, FAD binding protein
succinate:quinone oxidoreductase, membrane protein SdhC
succinate:quinone oxidoreductase, iron-sulfur cluster binding protein
succinate:quinone oxidoreductase, membrane protein SdhD
srlAEBD-gutM-srlR-gutQ 0.33 sorbitol PTS permease - SrlB subunit
sorbitol PTS permease - SrlA subunit
sorbitol PTS permease - SrlE subunit
sorbitol-6-phosphate dehydrogenase
D-arabinose 5-phosphate isomerase
GutR DNA-binding transcriptional repressor
GutM DNA-binding transcriptional activator
gntP 0.33 gluconate / fructuronate transporter GntP
hupB 0.31 transcriptional dual regulator HU-β, NS1 (HU-1)
rpoS 0.31 RNA polymerase, sigma S (sigma 38) factor
udp 0.30 uridine phosphorylase
nanA 0.29 N-acetylneuraminate lyase
secB-gpsA 0.29 glycerol-3-phosphate dehydrogenase
SecB chaperone
ivbL 0.29 ilvB operon leader peptide
flhDC 0.29 FlhC transcriptional dual regulator
FlhD transcriptional dual regulator
oxyR 0.27 OxyR DNA-binding transcriptional dual regulator
metK 0.27 methionine adenosyltransferase
gntX-nfuA 0.27 protein involved in utilization of DNA as a carbon source
iron-sulfur cluster scaffold protein
gltBDF 0.27 glutamate synthase, large subunit
glutamate synthase, small subunit
periplasmic protein
nupC 0.26 nucleoside:H+ symporter NupC
fumA 0.25 fumarase A
gntT 0.24 gluconate transporter GntT
glpFKX 0.24 glycerol channel GlpF
fructose 1,6-bisphosphatase II
glycerol kinase
fucPIKUR 0.24 L-fucose mutarotase
FucR transcriptional activator
L-fuculokinase
fucose:H+ symporter
L-fucose isomerase
rbsDACBKR 0.23 ribokinase
ribose ABC transporter - putative ATP binding subunit
ribose ABC transporter - membrane subunit
ribose ABC transporter - putative periplasmic binding protein
ribose pyranase
RbsR DNA-binding transcriptional dual regulator
sdhDAB 0.23 succinate:quinone oxidoreductase, FAD binding protein
succinate:quinone oxidoreductase, iron-sulfur cluster binding protein
succinate:quinone oxidoreductase, membrane protein SdhD
araFGH 0.23 arabinose ABC transporter - periplasmic binding protein
arabinose ABC transporter - ATP binding subunit
arabinose ABC transporter - membrane subunit
cytR 0.22 CytR DNA-binding transcriptional repressor
ycdZ 0.21 predicted inner membrane protein
tsx 0.21 nucleoside channel; receptor of phage T6 and colicin K
uxaB 0.21 altronate oxidoreductase
rpsF-priB-rpsR-rplI 0.20 30S ribosomal subunit protein S6
primosomal replication protein N
30S ribosomal subunit protein S18
50S ribosomal subunit protein L9
xylAB 0.19 xylose isomerase
xylulokinase
galETKM 0.19 galactose-1-phosphate uridylyltransferase
UDP-glucose 4-epimerase
galactose-1-epimerase
galactokinase
melR 0.19 MelR DNA-binding transcriptional dual regulator
agp 0.18 glucose-1-phosphatase
yhfA 0.18 conserved protein
tnaC 0.18 tryptophanase operon leader peptide
epd-pgk-fbaA 0.18 erythrose 4-phosphate dehydrogenase
phosphoglycerate kinase
fructose bisphosphate aldolase class II
sfsA-dksA 0.17 RNA polymerase-binding transcription factor DksA
predicted DNA-binding transcriptional regulator of maltose metabolism
spf 0.17 Spot42
ppiA 0.16 peptidyl-prolyl cis-trans isomerase A (rotamase A)
relA-mazEF 0.16 MazE antitoxin of the MazF-MazE toxin-antitoxin system
GDP pyrophosphokinase/GTP pyrophosphokinase
MazF toxin of the MazF-MazE toxin-antitoxin system that exhibits ribonuclease activity
cstA 0.16 peptide transporter induced by carbon starvation
glpEGR 0.15 thiosulfate sulfurtransferase
intramembrane serine protease GlpG
GlpR DNA-binding transcriptional repressor
sxy 0.15 transcriptional coactivator for CRP
galE 0.14 UDP-glucose 4-epimerase
fumC 0.14 fumarase C
idnDOTR 0.13 L-idonate 5-dehydrogenase
5-keto-D-gluconate 5-reductase
IdnR transcriptional regulator
L-idonate / 5-ketogluconate / gluconate transporter IdnT
murQP 0.13 N-acetylmuramic acid PTS permease / anhydro-N-acetylmuramic acid permease
N-acetylmuramic acid 6-phosphate etherase
aaeR 0.12 quorum sensing transcriptional regulator of LYSR-type
zraSR 0.12 ZraS sensory histidine kinase
ZraR transcriptional activator
acnB 0.12 bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase
yiaJ 0.12 YiaJ DNA-binding transcriptional repressor
fucAO 0.11 L-1,2-propanediol oxidoreductase
L-fuculose-phosphate aldolase
malT 0.11 MalT transcriptional activator
mlc 0.10 Mlc DNA-binding transcriptional repressor
rplM-rpsI 0.10 50S ribosomal subunit protein L13
30S ribosomal subunit protein S9
gcvTHP 0.10 glycine cleavage system H protein
glycine decarboxylase
aminomethyltransferase
dsdA 0.10 D-serine ammonia-lyase
galETK 0.10 galactose-1-phosphate uridylyltransferase
UDP-glucose 4-epimerase
galactokinase
exuT 0.09 hexuronate transporter
malXY 0.08 MalX PTS permease
bifunctional β-cystathionase, PLP-dependent and regulator of maltose regulon
pncB 0.08 nicotinate phosphoribosyltransferase
prpR 0.08 PrpR DNA-binding transcriptional dual regulator
aldB 0.08 acetaldehyde dehydrogenase
putP 0.07 proline:Na+ symporter
nagBAC-umpH 0.07 glucosamine-6-phosphate deaminase
NagC DNA-binding transcriptional dual regulator
UMP phosphatase
N-acetylglucosamine-6-phosphate deacetylase
epd-pgk 0.07 erythrose 4-phosphate dehydrogenase
phosphoglycerate kinase
malK-lamB-malM 0.06 maltose outer membrane porin / phage lambda receptor protein
maltose regulon periplasmic protein
maltose ABC transporter - ATP binding subunit
ivbL-ilvBN 0.06 acetohydroxy acid synthase I, large subunit
acetohydroxy acid synthase I, small subunit
ilvB operon leader peptide
mtlADR 0.06 MtlR DNA-binding transcriptional repressor
mannitol PTS permease
mannitol-1-phosphate 5-dehydrogenase
grpE 0.05 nucleotide exchange factor
araE 0.05 arabinose:H+ symporter
pdhR-aceEF-lpd 0.05 PdhR DNA-binding transcriptional dual regulator
lipoamide dehydrogenase
pyruvate dehydrogenase, E2 subunit
subunit of E1p component of pyruvate dehydrogenase complex
malI 0.04 MalI DNA-binding transcriptional repressor
yaeQ-arfB-nlpE 0.04 peptidyl-tRNA hydrolase, ribosome rescue factor
conserved protein
outer membrane lipoprotein NlpE, involved in surface sensing
focA-pflB 0.04 formate channel FocA
pyruvate formate-lyase (inactive)
araC 0.04 AraC DNA-binding transcriptional dual regulator
ampDE 0.04 N-acetyl-anhydromuramyl-L-alanine amidase
inner membrane protein
comR 0.03 ComR DNA-binding transcriptional repressor
aaeXAB 0.03 hydroxylated, aromatic carboxylic acid exporter - putative membrane fusion protein
hypothetical protein
hydroxylated, aromatic carboxylic acid exporter - putative membrane subunit
hfq-hflXKC 0.03 regulator of FtsH protease
RNA-binding protein that affects many cellular processes; homolog of mammalian Sm/Sm-like proteins
regulator of FtsH protease
ribosome-dissociating factor, GTPase
patZ 0.03 peptidyl-lysine acetyltransferase
malEFG 0.03 maltose ABC transporter - membrane subunit
maltose ABC transporter - membrane subunit
maltose ABC transporter - periplasmic binding protein
gadE-mdtEF 0.03 MdtEF-TolC multidrug efflux pump - permease subunit
MdtEF-TolC multidrug efflux pump - membrane fusion protein
GadE DNA-binding transcriptional activator
galET 0.02 galactose-1-phosphate uridylyltransferase
UDP-glucose 4-epimerase
dcuR 0.02 DcuR transcriptional activator
fumAC 0.02 fumarase A
fumarase C
bglGFB 0.01 6-phospho-β-glucosidase B; cryptic
BglG transcriptional antiterminator
BglF
cpdB 0.01 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase
galS 0.01 GalS DNA-binding transcriptional dual regulator
kbaZ-agaVWA 0.01 predicted truncated N-acetylgalactosamine-6-phosphate deacetylase
N-acetyl-D-galactosamine PTS permease (cryptic) - AgaW subunit (pseudogene)
N-acetyl-D-galactosamine PTS permease (cryptic) - AgaV subunit
tagatose-1,6-bisphosphate aldolase 1 subunit KbaZ
xylFGHR 0.01 xylose ABC transporter - membrane subunit
XylR transcriptional dual regulator
xylose ABC transporter - ATP binding subunit
xylose ABC transporter - periplasmic binding protein
araE-ygeA 0.00 predicted racemase
arabinose:H+ symporter

Network of associatons between targets according to the STRING database.

First level regulatory network of CRP

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
0.5 1.4 GO:0006208 pyrimidine nucleobase catabolic process(GO:0006208)
0.5 1.4 GO:0000303 response to superoxide(GO:0000303) superoxide metabolic process(GO:0006801)
0.4 1.1 GO:0006059 hexitol metabolic process(GO:0006059) hexitol catabolic process(GO:0019407)
0.3 1.0 GO:0051828 entry into host cell(GO:0030260) entry into host(GO:0044409) entry into cell of other organism involved in symbiotic interaction(GO:0051806) entry into other organism involved in symbiotic interaction(GO:0051828)
0.3 1.0 GO:0006108 malate metabolic process(GO:0006108)
0.3 1.0 GO:0015755 fructose transport(GO:0015755)
0.3 1.4 GO:0010675 regulation of cellular carbohydrate metabolic process(GO:0010675)
0.2 1.4 GO:0006094 gluconeogenesis(GO:0006094) hexose biosynthetic process(GO:0019319)
0.2 0.9 GO:0045900 negative regulation of translational elongation(GO:0045900)
0.2 0.7 GO:0006528 asparagine metabolic process(GO:0006528)
0.2 0.7 GO:0019464 glycine decarboxylation via glycine cleavage system(GO:0019464)
0.2 0.9 GO:0090357 regulation of cellular amino acid metabolic process(GO:0006521) regulation of cellular amine metabolic process(GO:0033238) regulation of tryptophan metabolic process(GO:0090357)
0.2 0.8 GO:0015858 nucleoside transport(GO:0015858)
0.2 1.0 GO:0006567 threonine catabolic process(GO:0006567)
0.2 0.6 GO:0046686 response to cadmium ion(GO:0046686)
0.2 0.6 GO:0005993 trehalose catabolic process(GO:0005993)
0.2 2.4 GO:0006099 tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101)
0.2 0.3 GO:0034214 protein hexamerization(GO:0034214)
0.1 0.4 GO:0042873 aldonate transport(GO:0042873)
0.1 0.6 GO:0009254 peptidoglycan turnover(GO:0009254)
0.1 1.2 GO:0006855 drug transmembrane transport(GO:0006855)
0.1 0.4 GO:0043242 negative regulation of protein complex disassembly(GO:0043242) negative regulation of DNA-templated transcription, termination(GO:0060567)
0.1 0.4 GO:0033499 galactose catabolic process via UDP-galactose(GO:0033499)
0.1 0.5 GO:0015750 pentose transport(GO:0015750)
0.1 0.3 GO:0043952 protein transport by the Sec complex(GO:0043952) chaperone-mediated protein transport(GO:0072321)
0.1 0.3 GO:0046498 S-adenosylmethionine cycle(GO:0033353) S-adenosylhomocysteine metabolic process(GO:0046498) S-adenosylmethionine metabolic process(GO:0046500)
0.1 0.4 GO:0005978 glycogen biosynthetic process(GO:0005978)
0.1 0.1 GO:0015931 nucleobase-containing compound transport(GO:0015931)
0.1 0.2 GO:0046348 N-acetylneuraminate metabolic process(GO:0006054) N-acetylneuraminate catabolic process(GO:0019262) amino sugar catabolic process(GO:0046348)
0.1 0.2 GO:0015768 maltose transport(GO:0015768)
0.1 0.2 GO:0015969 guanosine tetraphosphate metabolic process(GO:0015969) purine ribonucleoside bisphosphate metabolic process(GO:0034035) ncRNA catabolic process(GO:0034661)
0.1 0.4 GO:0009099 valine biosynthetic process(GO:0009099)
0.0 0.1 GO:0015976 carbon utilization(GO:0015976)
0.0 0.1 GO:0008156 negative regulation of DNA replication(GO:0008156) negative regulation of DNA metabolic process(GO:0051053)
0.0 0.5 GO:0006096 glycolytic process(GO:0006096)
0.0 0.2 GO:0006276 plasmid maintenance(GO:0006276)
0.0 0.1 GO:0046174 polyol catabolic process(GO:0046174)
0.0 0.1 GO:0006063 uronic acid metabolic process(GO:0006063)
0.0 0.1 GO:0097305 response to alcohol(GO:0097305)
0.0 0.1 GO:0010043 response to zinc ion(GO:0010043)
0.0 0.1 GO:0009071 serine family amino acid catabolic process(GO:0009071)
0.0 0.2 GO:0006352 DNA-templated transcription, initiation(GO:0006352)
0.0 0.1 GO:0072344 rescue of stalled ribosome(GO:0072344)
0.0 0.1 GO:0030490 maturation of SSU-rRNA(GO:0030490)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 2.2 GO:0046930 pore complex(GO:0046930)
0.2 0.6 GO:0045273 respiratory chain complex II(GO:0045273) plasma membrane respiratory chain complex II(GO:0045274)
0.2 0.5 GO:0009295 nucleoid(GO:0009295)
0.1 1.2 GO:0015935 small ribosomal subunit(GO:0015935) cytosolic small ribosomal subunit(GO:0022627)
0.1 1.4 GO:0019898 extrinsic component of membrane(GO:0019898)
0.0 0.3 GO:0005618 cell wall(GO:0005618)
0.0 9.3 GO:0005829 cytosol(GO:0005829)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.5 1.4 GO:0004784 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
0.3 0.3 GO:0019146 arabinose-5-phosphate isomerase activity(GO:0019146)
0.3 1.2 GO:0005469 succinate:fumarate antiporter activity(GO:0005469)
0.3 1.1 GO:0003954 NADH dehydrogenase activity(GO:0003954)
0.3 1.0 GO:0008861 formate C-acetyltransferase activity(GO:0008861)
0.2 1.1 GO:0005337 nucleoside transmembrane transporter activity(GO:0005337) nucleobase-containing compound transmembrane transporter activity(GO:0015932)
0.2 2.4 GO:0015288 porin activity(GO:0015288) wide pore channel activity(GO:0022829)
0.2 0.6 GO:0015927 trehalase activity(GO:0015927)
0.2 0.6 GO:0000104 succinate dehydrogenase activity(GO:0000104)
0.2 0.7 GO:0015128 gluconate transmembrane transporter activity(GO:0015128) aldonate transmembrane transporter activity(GO:0042879)
0.2 0.7 GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity(GO:0004365) glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity(GO:0043891)
0.2 0.8 GO:0016841 ammonia-lyase activity(GO:0016841)
0.2 0.5 GO:0043211 carbohydrate-transporting ATPase activity(GO:0043211)
0.2 1.3 GO:0030955 potassium ion binding(GO:0030955)
0.1 0.4 GO:0050308 sugar-phosphatase activity(GO:0050308)
0.1 0.4 GO:0019534 toxin transporter activity(GO:0019534)
0.1 0.4 GO:0009011 starch synthase activity(GO:0009011)
0.1 0.4 GO:0003978 UDP-glucose 4-epimerase activity(GO:0003978)
0.1 0.4 GO:0004333 fumarate hydratase activity(GO:0004333)
0.1 0.4 GO:0001070 RNA binding transcription factor activity(GO:0001070) transcription antitermination factor activity, RNA binding(GO:0001072)
0.1 0.2 GO:0070181 small ribosomal subunit rRNA binding(GO:0070181)
0.1 0.3 GO:0042900 fucose transmembrane transporter activity(GO:0015150) arabinose transmembrane transporter activity(GO:0042900)
0.1 0.6 GO:0005509 calcium ion binding(GO:0005509)
0.1 0.9 GO:0043024 ribosomal small subunit binding(GO:0043024)
0.1 0.6 GO:0008047 enzyme activator activity(GO:0008047)
0.1 0.6 GO:0015149 hexose transmembrane transporter activity(GO:0015149)
0.1 0.2 GO:0016859 peptidyl-prolyl cis-trans isomerase activity(GO:0003755) cis-trans isomerase activity(GO:0016859)
0.1 0.5 GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor(GO:0016668)
0.1 0.3 GO:0001000 bacterial-type RNA polymerase core enzyme binding(GO:0001000)
0.1 5.0 GO:0008270 zinc ion binding(GO:0008270)
0.1 0.4 GO:0003697 single-stranded DNA binding(GO:0003697)
0.1 0.5 GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides(GO:0016811)
0.1 0.2 GO:0008893 GTP diphosphokinase activity(GO:0008728) guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity(GO:0008893) diphosphoric monoester hydrolase activity(GO:0016794)
0.0 0.3 GO:0051082 unfolded protein binding(GO:0051082)
0.0 0.1 GO:0003984 acetolactate synthase activity(GO:0003984)
0.0 0.2 GO:0016783 sulfurtransferase activity(GO:0016783)
0.0 0.1 GO:0031405 lipoic acid binding(GO:0031405)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.2 PID ANGIOPOIETIN RECEPTOR PATHWAY Angiopoietin receptor Tie2-mediated signaling
0.1 0.2 NABA MATRISOME ASSOCIATED Ensemble of genes encoding ECM-associated proteins including ECM-affilaited proteins, ECM regulators and secreted factors

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 0.6 REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT Genes involved in The citric acid (TCA) cycle and respiratory electron transport
0.1 0.2 REACTOME DEVELOPMENTAL BIOLOGY Genes involved in Developmental Biology
0.0 0.4 REACTOME METABOLISM OF CARBOHYDRATES Genes involved in Metabolism of carbohydrates
0.0 0.1 REACTOME PLATELET ACTIVATION SIGNALING AND AGGREGATION Genes involved in Platelet activation, signaling and aggregation