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

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Results for PhoB

Z-value: 1.45

Transcription factors associated with PhoB

Gene Symbol Gene ID Gene Info
phoB
phoB PhoB transcriptional dual regulator

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
phoB-0.781.6e-06Click!

Activity profile of PhoB motif

Sorted Z-values of PhoB motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
ugpBAECQ 14.63
ugpE
ugpA
ugpB
ugpC
ugpQ
glycerol-3-phosphate ABC transporter - membrane subunit
glycerol-3-phosphate ABC transporter - membrane subunit
glycerol-3-phosphate ABC transporter - periplasmic binding protein
glycerol-3-phosphate ABC transporter - ATP binding subunit
glycerophosphodiester phosphodiesterase, cytosolic
phoA-psiF 14.29
phoA
psiF
alkaline phosphatase
conserved protein
pitB 12.07
pitB
metal phosphate:H+ symporter PitB
phoH 11.76
phoH
ATP-binding protein
pstS 11.01
pstS
phosphate ABC transporter - periplasmic binding protein
phoE 10.51
phoE
outer membrane porin E
yedX 10.21
yedX
hydroxyisourate hydrolase / transthyretin-related protein
adiC 9.88
adiC
AdiC arginine:agmatine antiporter
waaH 9.85
waaH
UDP-glucuronate:LPS(HepIII) glycosyltransferase
prpR 8.05
prpR
PrpR DNA-binding transcriptional dual regulator
pstSCA 7.76
pstS
pstC
pstA
phosphate ABC transporter - periplasmic binding protein
phosphate ABC transporter - membrane subunit
phosphate ABC transporter - membrane subunit
feaR 6.80
feaR
FeaR DNA-binding transcriptional activator
asr 5.80
asr
acid shock protein
phnCDE_1E_2FGHIJKLMNOP 4.88
phnP
phnL
phnF
phnG
phnD
phnC
phnO
phnN
phnE_1
phnE_2
phnM
phnJ
phnK
phnH
phnI
5-phospho-α-D-ribosyl 1,2-cyclic phosphate phosphodiesterase
PhnL subunit of methylphosphonate degradation complex
PhnF predicted transcriptional regulator
carbon-phosphorus lyase core complex, PhnG subunit
phosphonate ABC transporter - periplasmic binding protein
phosphonate ABC transporter - ATP binding subunit
aminoalkylphosphonate N-acetyltransferase
ribose 1,5-bisphosphokinase
phosphonate ABC transporter - membrane subunit
phosphonate/organophosphate ester transporter (pseudogene)
RPnTP hydrolase
carbon-phosphorus lyase core complex, PhnJ subunit
predicted carbon-phosphorus lyase subunit
carbon-phosphorus lyase core complex, PhnH subunit
carbon-phosphorus lyase core complex, PhnI subunit
gadX 4.28
gadX
GadX DNA-binding transcriptional dual regulator
phoBR 3.68
phoR
phoB
PhoR
PhoB transcriptional dual regulator
tktB 3.50
tktB
transketolase II
gadXW 3.33
gadW
gadX
GadW DNA-binding transcriptional dual regulator
GadX DNA-binding transcriptional dual regulator
phoU 3.26
phoU
negative regulator of the pho regulon
psiE 1.22
psiE
predicted phosphate starvation-inducible protein
yhjC 1.12
yhjC
predicted DNA-binding transcriptional regulator

Network of associatons between targets according to the STRING database.

First level regulatory network of PhoB

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
4.2 33.9 GO:0006817 phosphate ion transport(GO:0006817)
3.7 14.6 GO:0015748 organophosphate ester transport(GO:0015748)
2.7 13.5 GO:0016036 cellular response to phosphate starvation(GO:0016036)
2.5 9.9 GO:0045852 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)
1.7 10.2 GO:0006144 purine nucleobase metabolic process(GO:0006144)
1.6 4.9 GO:0046391 5-phosphoribose 1-diphosphate biosynthetic process(GO:0006015) 5-phosphoribose 1-diphosphate metabolic process(GO:0046391)
1.2 3.5 GO:0009052 pentose-phosphate shunt, non-oxidative branch(GO:0009052)
1.0 14.3 GO:0016311 dephosphorylation(GO:0016311)
0.4 5.8 GO:0001101 response to acid chemical(GO:0001101)
0.3 17.7 GO:0051254 positive regulation of transcription, DNA-templated(GO:0045893) positive regulation of RNA metabolic process(GO:0051254) positive regulation of RNA biosynthetic process(GO:1902680) positive regulation of nucleic acid-templated transcription(GO:1903508)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.2 14.6 GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing(GO:0055052)
0.7 4.9 GO:0061695 transferase complex, transferring phosphorus-containing groups(GO:0061695)
0.6 18.5 GO:1904949 ATP-binding cassette (ABC) transporter complex(GO:0043190) ATPase dependent transmembrane transport complex(GO:0098533) ATPase complex(GO:1904949)
0.3 3.3 GO:0019897 extrinsic component of plasma membrane(GO:0019897)
0.1 6.8 GO:0042597 periplasmic space(GO:0042597)
0.1 19.7 GO:0005887 integral component of plasma membrane(GO:0005887)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
4.9 14.6 GO:0015166 polyol transmembrane transporter activity(GO:0015166)
3.7 18.5 GO:0042301 phosphate ion binding(GO:0042301)
3.0 12.1 GO:0005315 inorganic phosphate transmembrane transporter activity(GO:0005315)
2.6 10.2 GO:0016812 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides(GO:0016812)
2.5 9.9 GO:0015181 arginine transmembrane transporter activity(GO:0015181)
1.2 9.8 GO:0008194 UDP-glycosyltransferase activity(GO:0008194)
1.2 3.7 GO:0001098 basal transcription machinery binding(GO:0001098) bacterial-type RNA polymerase holo enzyme binding(GO:0001108)
1.0 7.6 GO:0001140 transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding(GO:0001140)
0.8 4.9 GO:0008080 N-acetyltransferase activity(GO:0008080) phosphotransferase activity, phosphate group as acceptor(GO:0016776)
0.5 3.5 GO:0016744 transferase activity, transferring aldehyde or ketonic groups(GO:0016744)
0.5 6.8 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)
0.4 12.0 GO:0016791 phosphatase activity(GO:0016791)
0.2 11.8 GO:0005524 ATP binding(GO:0005524)
0.2 3.3 GO:0030145 manganese ion binding(GO:0030145)
0.1 4.5 GO:0003700 transcription factor activity, sequence-specific DNA binding(GO:0003700)