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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for Sigma28

Z-value: 3.10

Transcription factors associated with Sigma28

Gene Symbol Gene ID Gene Info
fliA
fliA RNA polymerase sigma factor FliA

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
fliZ0.801.8e-02Click!
fliA0.801.8e-02Click!

Activity profile of Sigma28 motif

Sorted Z-values of Sigma28 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
ynjH 17.30
ynjH
predicted protein
yhiL 15.21
yhiL
predicted protein
trg 13.07

ves 11.13
ves
conserved protein
flxA 10.24
flxA
Qin prophage; predicted protein
crfC-yjcZ 9.27
crfC
yjcZ
clamp-binding sister replication fork colocalization protein
conserved protein
aer 7.94
aer
aerotaxis sensor receptor, flavoprotein
tar-tap-cheRBYZ 7.69
cheR
cheZ
cheY
cheB
chemotaxis protein methyltransferase/chemotaxis protein methyltransferase/chemotaxis protein methyltransferase/chemotaxis protein methyltransferase/chemotaxis protein methyltransferase
CheZ
chemotaxis regulator transmitting signal to flagellar motor component
CheB
fliC 7.32
fliC
flagellar biosynthesis; flagellin, filament structural protein
fliDST 6.53
fliT
fliD
fliS
flagellar biosynthesis protein FliT
flagellar cap protein FliD; filament capping protein; enables filament assembly
flagellar biosynthesis protein FliS
pdeH 6.21
pdeH
c-di-GMP phosphodiesterase
yjcS 6.13
yjcS
alkyl sulfatase
motAB-cheAW 6.12
motA
motB
cheW
cheA
MotA protein, proton conductor component of motor; no effect on switching
MotB protein, enables flagellar motor rotation, linking torque machinery to cell wall
CheW
CheA(S)
tsr 5.37

flgKL 4.66
flgK
flgL
flagellar biosynthesis, hook-filament junction protein 1
flagellar biosynthesis; hook-filament junction protein
fliLMNOPQR 4.21
fliQ
fliP
fliR
fliM
fliL
fliO
fliN
flagellar biosynthesis protein FliQ
flagellar biosynthesis protein FliP
flagellar biosynthesis protein FliR
flagellar motor switch protein FliM
flagellar protein FliL
flagellar biosynthesis protein FliO
flagellar motor switch protein FliN
flgMN 3.50
flgN
flgM
flagellar biosynthesis protein FlgN
anti-sigma factor for FliA (σ28)
ycgR 3.25
ycgR
molecular brake that regulates flagellar motility in response to c-di-GMP
ygbK 1.89
ygbK
conserved protein
yecF 1.77
yecF
predicted protein
fliE 1.63
fliE
flagellar basal-body protein FliE
modABC 1.47
modA
modB
modC
molybdate ABC transporter - periplasmic binding protein
molybdate ABC transporter - membrane subunit
molybdate ABC transporter - ATP binding subunit
fliFGHIJK 1.43
fliI
fliH
fliK
fliJ
fliG
fliF
flagellum-specific ATP synthase FliI
flagellar biosynthesis protein FliH
flagellar hook-length control protein FliK
flagellar biosynthesis protein FliJ
flagellar motor switch protein FliG
flagellar M-ring protein FliF; basal-body MS(membrane and supramembrane)-ring and collar protein

Network of associatons between targets according to the STRING database.

First level regulatory network of Sigma28

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
3.0 12.2 GO:0050918 positive chemotaxis(GO:0050918)
2.8 13.8 GO:0042330 chemotaxis(GO:0006935) taxis(GO:0042330)
1.2 4.7 GO:0044781 bacterial-type flagellum assembly(GO:0044780) bacterial-type flagellum organization(GO:0044781)
1.2 9.3 GO:0007059 chromosome segregation(GO:0007059)
0.9 15.7 GO:0097588 cilium or flagellum-dependent cell motility(GO:0001539) bacterial-type flagellum-dependent cell motility(GO:0071973) archaeal or bacterial-type flagellum-dependent cell motility(GO:0097588)
0.7 3.5 GO:0030162 regulation of proteolysis(GO:0030162)
0.7 6.1 GO:0006805 xenobiotic metabolic process(GO:0006805) response to xenobiotic stimulus(GO:0009410) cellular response to xenobiotic stimulus(GO:0071466)
0.1 1.5 GO:0015698 inorganic anion transport(GO:0015698)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
3.0 12.2 GO:0044461 bacterial-type flagellum part(GO:0044461) cell projection part(GO:0044463)
0.1 4.4 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)
0.0 15.0 GO:0005886 plasma membrane(GO:0005886)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.2 6.2 GO:0071111 cyclic-guanylate-specific phosphodiesterase activity(GO:0071111)
0.7 3.3 GO:0035438 cyclic nucleotide binding(GO:0030551) cyclic-di-GMP binding(GO:0035438)
0.5 7.7 GO:0004721 phosphoprotein phosphatase activity(GO:0004721)
0.4 7.9 GO:0004871 signal transducer activity(GO:0004871)
0.2 1.5 GO:0043225 molybdenum ion binding(GO:0030151) anion transmembrane-transporting ATPase activity(GO:0043225)
0.2 1.8 GO:0016989 sigma factor antagonist activity(GO:0016989)
0.1 5.9 GO:0016788 hydrolase activity, acting on ester bonds(GO:0016788)
0.0 14.4 GO:0005515 protein binding(GO:0005515)