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

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Results for Fis

Z-value: 2.81

Transcription factors associated with Fis

Gene Symbol Gene ID Gene Info
fis
fis Fis DNA-binding transcriptional dual regulator

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
fis-0.896.6e-10Click!

Activity profile of Fis motif

Sorted Z-values of Fis motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
rrsE-gltV-rrlE-rrfE 24.35
rrlE
gltV
rrsE
rrfE
rrlE 23S ribosomal RNA
tRNAgltV
rrsE 16S ribosomal RNA
rrfE 5S ribosomal RNA
argW 22.79
argW
tRNAargW
rrsB-gltT-rrlB-rrfB 21.37
rrlB
gltT
rrfB
rrsB
rrlB 23S ribosomal RNA
tRNAgltT
rrfB 5S ribosomal RNA
rrsB 16S ribosomal RNA
glpABC 20.95
glpA
glpC
glpB
anaerobic glycerol-3-phosphate dehydrogenase subunit A
anaerobic glycerol-3-phosphate dehydrogenase subunit C
anaerobic glycerol-3-phosphate dehydrogenase subunit B
rrsA-ileT-alaT-rrlA-rrfA 20.80
rrlA
ileT
alaT
rrsA
rrfA
23S ribosomal RNA (rrlA)
tRNAileT
tRNAalaT
16S ribosomal RNA (rrsA)
5S ribosomal RNA (rrfA)
rrsC-gltU-rrlC-rrfC 20.19
rrlC
gltU
rrfC
rrsC
rrlC 23S ribosomal RNA
tRNAgltU
rrfC 5S ribosomal RNA
rrsC 16S ribosomal RNA
ssrS 20.12
ssrS
6S RNA
ssrS-fau 20.10
ssrS
fau
6S RNA
5-formyltetrahydrofolate cyclo-ligase
leuX 20.02
leuX
tRNAleuX
rrsG-gltW-rrlG-rrfG 19.73
rrlG
gltW
rrfG
rrsG
rrlG 23S ribosomal RNA
tRNAgltW
rrfG 5S ribosomal RNA
rrsG 16S ribosomal RNA
patA 19.30
patA
putrescine aminotransferase
thrW 18.76
thrW
tRNAthrW
argU 18.40
argU
tRNAargU
pheU 18.37
pheU
tRNApheU
pheV 18.37
pheV
tRNApheV
fumB 18.33
fumB
fumarase B
serT 18.23
serT
tRNASer1
metY 17.25
metY
tRNAfMet2
narK 17.10
narK
nitrate:nitrite antiporter NarK
alaWX 17.08
alaX
alaW
tRNAalaX
tRNAalaW
proL 17.06
proL
tRNAproL
valUXY-lysV 16.99
valY
valX
lysV
valU
tRNAvalY
tRNAvalX
tRNAlysV
tRNAvalU
nanA 16.99
nanA
N-acetylneuraminate lyase
rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF 16.99
rrlD
ileU
alaU
thrV
rrfF
rrsD
rrfD
rrlD 23S ribosomal RNA
tRNAileU
tRNAalaU
tRNAthrV
rrfF 5S ribosomal RNA
rrsD 16S ribosomal RNA
rrfD 5S ribosomal RNA
thrU-tyrU-glyT-thrT-tufB 16.96
tufB
thrT
thrU
glyT
tyrU
elongation factor Tu
tRNAthrT
tRNAthrU
tRNAglyT
tRNAtyrU
serX 16.93
serX
tRNASer5
glyU 16.87
glyU
tRNAglyU
tyrTV-tpr 16.70
tpr
tyrV
tyrT
predicted protamine-like protein
tRNAtyrV
tRNAtyrT
rrsH-ileV-alaV-rrlH-rrfH 16.36
rrlH
rrfH
rrsH
ileV
alaV
rrlH 23S ribosomal RNA
rrfH 5S ribosomal RNA
rrsH 16S ribosomal RNA
tRNAileV
tRNAalaV
argX-hisR-leuT-proM 15.77
argX
leuT
proM
hisR
tRNAargX
tRNAleuT
tRNAproM
tRNAhisR
metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp 15.43
metY
rimP
rpsO
pnp
rbfA
infB
nusA
truB
tRNAfMet2
ribosome maturation factor RimP
30S ribosomal subunit protein S15
polynucleotide phosphorylase
30S ribosome binding factor
protein chain initiation factor IF2
transcription termination/antitermination L factor
tRNA pseudouridine 55 synthase
metT-leuW-glnUW-metU-glnVX 14.69
metT
metU
leuW
glnX
glnW
glnV
glnU
tRNAmetT
tRNAmetU
tRNAleuW
tRNAGln2
tRNAGln1
tRNAGln2
tRNAGln1
proK 14.56
proK
tRNAproK
metY-rimP-nusA-infB 14.43
metY
rimP
infB
nusA
tRNAfMet2
ribosome maturation factor RimP
protein chain initiation factor IF2
transcription termination/antitermination L factor
lysT-valT-lysW 14.20
lysW
lysT
valT
tRNAlysW
tRNAlysT
tRNAvalT
aspV 13.84
aspV
tRNAaspV
nanATEK-yhcH 12.65
nanA
nanK
nanE
nanT
yhcH
N-acetylneuraminate lyase
N-acetylmannosamine kinase
predicted N-acetylmannosamine-6-phosphate epimerase
N-acetylneuraminate:H+ symporter
conserved protein
yeaR-yoaG 11.51
yoaG
yeaR
predicted protein
conserved protein
leuQPV 11.47
leuV
leuP
leuQ
tRNAleuV
tRNAleuP
tRNAleuQ
pyrD 10.60
pyrD
dihydroorotate dehydrogenase, type 2
mtlADR 8.85
mtlR
mtlA
mtlD
MtlR DNA-binding transcriptional repressor
mannitol PTS permease
mannitol-1-phosphate 5-dehydrogenase
narGHJI 8.85
narG
narI
narH
narJ
nitrate reductase A, α subunit
nitrate reductase A, γ subunit
nitrate reductase A, β subunit
molybdenum cofactor assembly chaperone subunit (δ subunit) of nitrate reductase 1
katE 8.26
katE
catalase II
hlyE 8.23
hlyE
hemolysin E
osmY 8.10
osmY
periplasmic chaperone, osmotically induced
gadBC 8.02
gadB
gadC
glutamate decarboxylase B subunit
glutamic acid:4-aminobutyrate antiporter
ansB 7.96
ansB
asparaginase II
marRAB 7.45
marB
marA
marR
multiple antibiotic resistance protein
MarA DNA-binding transcriptional dual regulator
MarR DNA-binding transcriptional repressor
rnpB 7.11
rnpB
RnpB
aldB 6.72
aldB
acetaldehyde dehydrogenase
trg 6.15

dmsABC 5.81
dmsA
dmsB
dmsC
dimethyl sulfoxide reductase, chain A
dimethyl sulfoxide reductase, chain B
dimethyl sulfoxide reductase, chain C
glcC 5.35
glcC
GlcC transcriptional dual regulator
fadBA 4.60
fadB
fadA
dodecenoyl-CoA δ-isomerase, enoyl-CoA hydratase, 3-hydroxybutyryl-CoA epimerase, 3-hydroxyacyl-CoA dehydrogenase
3-ketoacyl-CoA thiolase
glpTQ 2.90
glpT
glpQ
glycerol-3-phosphate:phosphate antiporter
glycerophosphoryl diester phosphodiesterase, periplasmic
mglAC 2.19
mglA
mglC
D-galactose / D-galactoside ABC transporter - ATP binding subunit
D-galactose / D-galactoside ABC transporter - membrane subunit
xylFGHR 2.10
xylH
xylR
xylG
xylF
xylose ABC transporter - membrane subunit
XylR transcriptional dual regulator
xylose ABC transporter - ATP binding subunit
xylose ABC transporter - periplasmic binding protein
cbpAM 2.04
cbpM
cbpA
chaperone modulator protein CbpM
chaperone with DnaK; curved DNA-binding protein
acs-yjcH-actP 1.86
acs
actP
yjcH
acetyl-CoA synthetase (AMP-forming)
acetate / glycolate : cation symporter
conserved inner membrane protein
cspI 1.18
cspI
Qin prophage; cold shock protein
ogt 0.60
ogt
O6-alkylguanine-DNA-alkyltransferase
hyaABCDEF 0.60
hyaB
hyaC
hyaA
hyaF
hyaD
hyaE
hydrogenase 1, large subunit
hydrogenase 1, b-type cytochrome subunit
hydrogenase 1, small subunit
protein involved in nickel incorporation into hydrogenase 1 proteins
protein involved in processing of HyaA and HyaB proteins
protein involved in quality control of HyaA

Network of associatons between targets according to the STRING database.

First level regulatory network of Fis

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
7.4 29.6 GO:0019262 N-acetylneuraminate metabolic process(GO:0006054) N-acetylneuraminate catabolic process(GO:0019262)
6.7 20.1 GO:0035999 tetrahydrofolate interconversion(GO:0035999)
5.1 15.4 GO:0031119 pseudouridine synthesis(GO:0001522) tRNA pseudouridine synthesis(GO:0031119) RNA 3'-end processing(GO:0031123)
3.8 11.5 GO:0015707 nitrite transport(GO:0015707)
3.2 19.3 GO:0006598 polyamine catabolic process(GO:0006598) putrescine catabolic process(GO:0009447)
3.0 8.9 GO:0019407 hexitol metabolic process(GO:0006059) hexitol catabolic process(GO:0019407)
3.0 8.9 GO:0071941 nitrogen cycle metabolic process(GO:0071941)
2.7 8.2 GO:0001906 cell killing(GO:0001906) cytolysis(GO:0019835) killing of cells of other organism(GO:0031640) modification of morphology or physiology of other organism(GO:0035821) disruption of cells of other organism(GO:0044364) cytolysis in other organism(GO:0051715)
2.7 8.0 GO:0006528 asparagine metabolic process(GO:0006528)
2.4 14.4 GO:0031564 transcription antitermination(GO:0031564)
2.2 6.7 GO:0097305 response to alcohol(GO:0097305)
1.5 2.9 GO:0015791 polyol transport(GO:0015791)
1.2 13.4 GO:0046434 organophosphate catabolic process(GO:0046434)
1.0 8.3 GO:0072593 reactive oxygen species metabolic process(GO:0072593)
0.9 1.9 GO:0043687 post-translational protein modification(GO:0043687)
0.8 7.4 GO:0097237 cellular response to antibiotic(GO:0071236) cellular response to toxic substance(GO:0097237)
0.8 4.0 GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process(GO:0006207) pyrimidine nucleobase biosynthetic process(GO:0019856)
0.7 2.2 GO:0015765 methylgalactoside transport(GO:0015765)
0.6 18.3 GO:0042710 biofilm formation(GO:0042710)
0.5 8.1 GO:0061077 chaperone-mediated protein folding(GO:0061077)
0.5 4.6 GO:0006635 fatty acid beta-oxidation(GO:0006635)
0.3 2.1 GO:0015750 pentose transport(GO:0015750)
0.1 0.6 GO:0035510 DNA dealkylation involved in DNA repair(GO:0006307) DNA dealkylation(GO:0035510)
0.1 0.6 GO:0016485 protein processing(GO:0016485)
0.0 0.2 GO:0051454 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
3.0 8.9 GO:0031235 intrinsic component of the cytoplasmic side of the plasma membrane(GO:0031235)
2.1 6.4 GO:0031237 intrinsic component of periplasmic side of plasma membrane(GO:0031237)
2.1 8.2 GO:0005576 extracellular region(GO:0005576)
0.1 9.9 GO:0042597 periplasmic space(GO:0042597)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
7.0 20.9 GO:0016901 oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor(GO:0016901)
6.0 29.9 GO:0097216 guanosine tetraphosphate binding(GO:0097216)
5.0 20.1 GO:0016882 cyclo-ligase activity(GO:0016882)
4.2 12.7 GO:0015136 sialic acid transmembrane transporter activity(GO:0015136)
3.8 11.5 GO:0015113 nitrite transmembrane transporter activity(GO:0015113)
3.7 18.3 GO:0004333 fumarate hydratase activity(GO:0004333)
3.5 10.6 GO:0016635 oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor(GO:0016635)
2.8 8.3 GO:0004096 catalase activity(GO:0004096)
2.2 8.9 GO:0016530 nitrate reductase activity(GO:0008940) metallochaperone activity(GO:0016530)
2.1 17.0 GO:0016833 oxo-acid-lyase activity(GO:0016833)
1.5 4.6 GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity(GO:0003857)
1.1 19.3 GO:0008483 transaminase activity(GO:0008483)
1.1 6.7 GO:0004029 aldehyde dehydrogenase (NAD) activity(GO:0004029)
1.0 2.9 GO:0015166 polyol transmembrane transporter activity(GO:0015166)
0.7 2.2 GO:0015592 methylgalactoside transmembrane transporter activity(GO:0015592)
0.6 1.9 GO:0015563 uptake transmembrane transporter activity(GO:0015563)
0.6 8.0 GO:0015297 antiporter activity(GO:0015297)
0.6 0.6 GO:0005048 signal sequence binding(GO:0005048)
0.5 8.0 GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides(GO:0016811)
0.3 2.1 GO:0015146 pentose transmembrane transporter activity(GO:0015146) monosaccharide binding(GO:0048029)
0.2 2.0 GO:0004857 enzyme inhibitor activity(GO:0004857)
0.1 0.6 GO:0008172 S-methyltransferase activity(GO:0008172)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
9.2 36.8 REACTOME INFLUENZA LIFE CYCLE Genes involved in Influenza Life Cycle
5.1 15.4 REACTOME PURINE SALVAGE Genes involved in Purine salvage