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

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Results for PhoP

Z-value: 0.71

Transcription factors associated with PhoP

Gene Symbol Gene ID Gene Info
phoP
phoP PhoP

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
phoP0.696.2e-05Click!

Activity profile of PhoP motif

Sorted Z-values of PhoP motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
borD 7.13
borD
lipoprotein bor homolog from lambdoid prophage DLP12
phoPQ 5.77
phoQ
phoP
PhoQ sensory histidine kinase
PhoP
ompT 5.13
ompT
outer membrane protease VII (outer membrane protein 3b)
mgtLA 4.16
mgtA
mgtL
Mg2+ / Ni2+ transporting ATPase
predicted leader peptide
rstAB 3.93
rstA
rstB
RstA transcriptional regulator
RstB sensory histidine kinase
yneM 3.72
yneM
small membrane protein
yrbL 3.56
yrbL
predicted protein
hemL 2.65
hemL
glutamate-1-semialdehyde aminotransferase
purHD 1.84
purH
purD
AICAR transformylase/IMP cyclohydrolase
phosphoribosylamine-glycine ligase
acrAB 1.77
acrB
acrA
AcrAB-TolC multidrug efflux pump - permease subunit
AcrAB-TolC multidrug efflux pump - membrane fusion protein
glgBXCAP 1.71
glgX
glgA
glgB
glgC
glgP
limit dextrin α-1,6-glucohydrolase
glycogen synthase
1,4-α-glucan branching enzyme
glucose-1-phosphate adenylyltransferase
glycogen phosphorylase
glgAP 1.61
glgP
glgA
glycogen phosphorylase
glycogen synthase
tolC-ygiABC 1.56
ygiC
ygiB
ygiA
tolC
predicted enzyme with ATPase activity
conserved outer membrane protein
predicted protein
TolC outer membrane channel
nagA 1.49
nagA
N-acetylglucosamine-6-phosphate deacetylase
mgrR 1.43
mgrR
MgrR
ydeP 0.92
ydeP
acid resistance protein
slyB 0.70
slyB
outer membrane lipoprotein
mgrB 0.47
mgrB
negative feedback regulator of the PhoQP system
ybjG 0.29
ybjG
undecaprenyl pyrophosphate phosphatase

Network of associatons between targets according to the STRING database.

First level regulatory network of PhoP

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
1.9 7.6 GO:0032026 response to magnesium ion(GO:0032026)
0.8 4.2 GO:0031556 transcriptional attenuation by ribosome(GO:0031556)
0.8 3.9 GO:0018106 peptidyl-histidine phosphorylation(GO:0018106) peptidyl-histidine modification(GO:0018202)
0.7 3.3 GO:0005978 glycogen biosynthetic process(GO:0005978) glycogen catabolic process(GO:0005980)
0.5 2.6 GO:0006782 protoporphyrinogen IX biosynthetic process(GO:0006782)
0.4 1.5 GO:0006054 N-acetylneuraminate metabolic process(GO:0006054) N-acetylneuraminate catabolic process(GO:0019262)
0.3 5.8 GO:0000160 phosphorelay signal transduction system(GO:0000160)
0.3 1.6 GO:0015891 siderophore transport(GO:0015891)
0.2 1.8 GO:0006855 drug transmembrane transport(GO:0006855)
0.2 5.1 GO:0006508 proteolysis(GO:0006508)
0.2 1.8 GO:0006164 purine nucleotide biosynthetic process(GO:0006164)
0.0 0.3 GO:0046677 response to antibiotic(GO:0046677)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.8 7.1 GO:0031225 anchored component of membrane(GO:0031225)
1.0 4.2 GO:0043231 membrane-bounded organelle(GO:0043227) intracellular membrane-bounded organelle(GO:0043231)
0.3 5.1 GO:0031230 intrinsic component of cell outer membrane(GO:0031230)
0.1 3.3 GO:1902495 transmembrane transporter complex(GO:1902495) transporter complex(GO:1990351)
0.0 9.5 GO:0016021 integral component of membrane(GO:0016021)
0.0 6.1 GO:0005829 cytosol(GO:0005829)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.1 3.3 GO:0009011 starch synthase activity(GO:0009011)
0.7 5.1 GO:0004252 serine-type endopeptidase activity(GO:0004252)
0.7 4.2 GO:0019829 cation-transporting ATPase activity(GO:0019829)
0.6 1.8 GO:0015307 drug:proton antiporter activity(GO:0015307)
0.5 9.7 GO:0004673 phosphorelay sensor kinase activity(GO:0000155) protein histidine kinase activity(GO:0004673)
0.5 1.8 GO:0019238 cyclohydrolase activity(GO:0019238)
0.3 1.6 GO:0015562 efflux transmembrane transporter activity(GO:0015562)
0.2 1.5 GO:0019213 deacetylase activity(GO:0019213)
0.2 2.6 GO:0016866 intramolecular transferase activity(GO:0016866)
0.1 0.3 GO:0050380 undecaprenyl-diphosphatase activity(GO:0050380)