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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for Fis

Z-value: 4.25

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
fis0.921.1e-03Click!

Activity profile of Fis motif

Sorted Z-values of Fis motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
ssrS 22.71
ssrS
6S RNA
rnpB 19.26
rnpB
RnpB
rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF 17.05
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
rrsC-gltU-rrlC-rrfC 16.82
rrlC
gltU
rrfC
rrsC
rrlC 23S ribosomal RNA
tRNAgltU
rrfC 5S ribosomal RNA
rrsC 16S ribosomal RNA
pflB 16.19
pflB
pyruvate formate-lyase (inactive)
rrsG-gltW-rrlG-rrfG 15.94
rrlG
gltW
rrfG
rrsG
rrlG 23S ribosomal RNA
tRNAgltW
rrfG 5S ribosomal RNA
rrsG 16S ribosomal RNA
rrsE-gltV-rrlE-rrfE 15.25
rrlE
gltV
rrsE
rrfE
rrlE 23S ribosomal RNA
tRNAgltV
rrsE 16S ribosomal RNA
rrfE 5S ribosomal RNA
rrsH-ileV-alaV-rrlH-rrfH 14.47
rrlH
rrfH
rrsH
ileV
alaV
rrlH 23S ribosomal RNA
rrfH 5S ribosomal RNA
rrsH 16S ribosomal RNA
tRNAileV
tRNAalaV
rrsB-gltT-rrlB-rrfB 14.43
rrlB
gltT
rrfB
rrsB
rrlB 23S ribosomal RNA
tRNAgltT
rrfB 5S ribosomal RNA
rrsB 16S ribosomal RNA
rrsA-ileT-alaT-rrlA-rrfA 14.30
rrlA
ileT
alaT
rrsA
rrfA
23S ribosomal RNA (rrlA)
tRNAileT
tRNAalaT
16S ribosomal RNA (rrsA)
5S ribosomal RNA (rrfA)
thrU-tyrU-glyT-thrT-tufB 14.25
tufB
thrT
thrU
glyT
tyrU
elongation factor Tu
tRNAthrT
tRNAthrU
tRNAglyT
tRNAtyrU
thrW 14.23
thrW
tRNAthrW
crp 11.22
crp
CRP transcriptional dual regulator
hupA 10.98
hupA
transcriptional dual regulator HU-α (HU-2)
dps 10.73
dps
stationary phase nucleoid protein that sequesters iron and protects DNA from damage
rplM-rpsI 10.27
rplM
rpsI
50S ribosomal subunit protein L13
30S ribosomal subunit protein S9
ansB 9.42
ansB
asparaginase II
hupB 9.11
hupB
transcriptional dual regulator HU-β, NS1 (HU-1)
argU 9.09
argU
tRNAargU
proK 8.79
proK
tRNAproK
serX 8.65
serX
tRNASer5
lpd 8.41
lpd
lipoamide dehydrogenase
glnA 7.67
glnA
glutamine synthetase
sra 7.58
sra
30S ribosomal subunit protein S22
gyrA 7.54
gyrA
DNA gyrase, subunit A
gyrB 6.23
gyrB
DNA gyrase, subunit B
nrdAB-yfaE 6.07
nrdA
nrdB
yfaE
ribonucleoside diphosphate reductase 1, α subunit
ribonucleoside diphosphate reductase 1, β subunit, ferritin-like
2Fe-2S cluster-containing protein involved in diferric-tyrosyl radical cofactor maintenance
gltX 6.01
gltX
glutamate-tRNA ligase
adhE 4.99
adhE
aldehyde-alcohol dehydrogenase
narK 4.94
narK
nitrate:nitrite antiporter NarK
narGHJI 4.73
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
cspA 4.66
cspA
CspA DNA-binding transcriptional activator
dusB-fis 4.57
fis
dusB
Fis DNA-binding transcriptional dual regulator
tRNA-dihydrouridine synthase B
metY-rimP-nusA-infB 4.25
metY
rimP
infB
nusA
tRNAfMet2
ribosome maturation factor RimP
protein chain initiation factor IF2
transcription termination/antitermination L factor
glnQ 4.12
glnQ
L-glutamine ABC transporter - ATP binding subunit
grcA 3.74
grcA
stress-induced alternate pyruvate formate-lyase subunit
metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp 3.50
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
fumB 3.47
fumB
fumarase B
pdxA-rsmA 3.46
pdxA
rsmA
4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent
16S rRNA m62A1518,m62A1519 dimethyltransferase
queA 3.34
queA
S-adenosylmethionine:tRNA ribosyltransferase-isomerase
nuoABCEFGHIJKLMN 3.26
nuoB
nuoC
nuoA
nuoF
nuoG
nuoE
nuoJ
nuoK
nuoH
nuoI
nuoN
nuoL
nuoM
NADH:ubiquinone oxidoreductase, chain B
NADH:ubiquinone oxidoreductase, chain CD
NADH:ubiquinone oxidoreductase, membrane subunit A
NADH:ubiquinone oxidoreductase, chain F
NADH:ubiquinone oxidoreductase, chain G
NADH:ubiquinone oxidoreductase, chain E
NADH:ubiquinone oxidoreductase, membrane subunit J
NADH:ubiquinone oxidoreductase, membrane subunit K
NADH:ubiquinone oxidoreductase, membrane subunit H
NADH:ubiquinone oxidoreductase, chain I
NADH:ubiquinone oxidoreductase, membrane subunit N
NADH:ubiquinone oxidoreductase, membrane subunit L
NADH:ubiquinone oxidoreductase, membrane subunit M
hns 3.17
hns
H-NS DNA-binding transcriptional dual regulator
nanA 3.01
nanA
N-acetylneuraminate lyase
mazEFG 2.06
mazE
mazF
mazG
MazE antitoxin of the MazF-MazE toxin-antitoxin system
MazF toxin of the MazF-MazE toxin-antitoxin system that exhibits ribonuclease activity
nucleoside triphosphate pyrophosphohydrolase
pdxA-rsmA-apaGH 1.94
apaG
pdxA
rsmA
apaH
hypothetical protein
4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent
16S rRNA m62A1518,m62A1519 dimethyltransferase
diadenosine tetraphosphatase
nrfABCDEFG 1.92
nrfF
nrfG
nrfD
nrfE
nrfB
nrfC
nrfA
activator of formate-dependent nitrite reductase complex
NrfG
formate dependent nitrite reductase - NrfD subunit
formate-dependent nitrite reductase; possible assembly function
formate-dependent nitrite reductase - penta-heme cytochrome c
formate-dependent nitrite reductase, 4Fe-4S subunit
formate dependent nitrite reductase - NrfA subunit
msrA 1.79
msrA
methionine sulfoxide reductase A
serT 1.50
serT
tRNASer1
guaBA 1.20
guaB
guaA
IMP dehydrogenase
GMP synthetase
acnB 1.01
acnB
bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase
glnALG 1.00
glnL
glnA
glnG
NtrB
glutamine synthetase
NtrC transcriptional dual regulator
osmY 0.31
osmY
periplasmic chaperone, osmotically induced
bglG 0.30
bglG
BglG transcriptional antiterminator

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
4.0 19.9 GO:0006567 threonine catabolic process(GO:0006567)
3.1 9.4 GO:0009068 asparagine metabolic process(GO:0006528) aspartate family amino acid catabolic process(GO:0009068)
2.9 8.7 GO:0019676 ammonia assimilation cycle(GO:0019676)
2.8 11.2 GO:0007584 response to nutrient(GO:0007584)
2.8 8.4 GO:0019464 glycine decarboxylation via glycine cleavage system(GO:0019464)
2.8 13.8 GO:0030490 maturation of SSU-rRNA(GO:0030490)
2.2 6.6 GO:0019645 anaerobic electron transport chain(GO:0019645)
2.1 2.1 GO:0019692 pyrimidine deoxyribonucleotide metabolic process(GO:0009219) 2'-deoxyribonucleotide metabolic process(GO:0009394) deoxyribose phosphate metabolic process(GO:0019692)
1.7 5.0 GO:0006067 ethanol metabolic process(GO:0006067)
1.6 9.6 GO:0000028 ribosomal small subunit assembly(GO:0000028)
1.6 4.7 GO:0043242 negative regulation of protein complex disassembly(GO:0043242) negative regulation of DNA-templated transcription, termination(GO:0060567)
1.0 6.1 GO:0009263 deoxyribonucleotide biosynthetic process(GO:0009263)
0.8 6.2 GO:0007059 chromosome segregation(GO:0007059)
0.7 3.3 GO:0002097 tRNA wobble base modification(GO:0002097)
0.5 2.1 GO:0019262 N-acetylneuraminate metabolic process(GO:0006054) N-acetylneuraminate catabolic process(GO:0019262)
0.4 1.8 GO:0030091 protein repair(GO:0030091)
0.4 1.2 GO:1901070 GMP biosynthetic process(GO:0006177) GMP metabolic process(GO:0046037) GTP metabolic process(GO:0046039) guanosine-containing compound biosynthetic process(GO:1901070)
0.3 10.7 GO:0042594 response to starvation(GO:0042594)
0.3 1.0 GO:0019626 glyoxylate cycle(GO:0006097) propionate metabolic process(GO:0019541) short-chain fatty acid catabolic process(GO:0019626)
0.3 6.0 GO:0043039 tRNA aminoacylation for protein translation(GO:0006418) tRNA aminoacylation(GO:0043039)
0.3 3.5 GO:0006099 tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101)
0.3 7.5 GO:0042493 response to drug(GO:0042493)
0.2 0.5 GO:0015707 nitrite transport(GO:0015707)
0.1 4.6 GO:0009314 response to radiation(GO:0009314)
0.0 0.3 GO:0061077 chaperone-mediated protein folding(GO:0061077)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
5.7 17.2 GO:0009295 nucleoid(GO:0009295)
1.6 8.0 GO:0098803 respiratory chain(GO:0070469) plasma membrane respiratory chain(GO:0070470) respiratory chain complex(GO:0098803)
1.3 21.4 GO:0015935 small ribosomal subunit(GO:0015935) cytosolic small ribosomal subunit(GO:0022627)
1.1 4.6 GO:0044427 chromosome(GO:0005694) chromosomal part(GO:0044427)
0.4 6.1 GO:0044445 cytosolic part(GO:0044445)
0.1 37.9 GO:0005829 cytosol(GO:0005829)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
5.0 19.9 GO:0008861 formate C-acetyltransferase activity(GO:0008861)
2.2 8.7 GO:0016211 ammonia ligase activity(GO:0016211)
2.0 6.1 GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor(GO:0004748) oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor(GO:0016728) ribonucleoside-diphosphate reductase activity(GO:0061731)
1.8 5.4 GO:0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity(GO:0000179) rRNA (adenine) methyltransferase activity(GO:0016433)
1.6 7.8 GO:0097216 guanosine tetraphosphate binding(GO:0097216)
1.3 10.3 GO:0070180 large ribosomal subunit rRNA binding(GO:0070180)
1.2 8.4 GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor(GO:0016668)
1.2 4.7 GO:0008940 nitrate reductase activity(GO:0008940) metallochaperone activity(GO:0016530)
1.2 4.7 GO:0001072 RNA binding transcription factor activity(GO:0001070) transcription antitermination factor activity, RNA binding(GO:0001072)
1.1 13.8 GO:0008094 DNA-dependent ATPase activity(GO:0008094)
0.9 2.8 GO:0008137 NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
0.7 4.9 GO:0015562 efflux transmembrane transporter activity(GO:0015562)
0.7 3.5 GO:0004333 fumarate hydratase activity(GO:0004333)
0.5 2.1 GO:0047429 nucleoside-triphosphate diphosphatase activity(GO:0047429)
0.5 9.4 GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides(GO:0016811)
0.5 1.9 GO:0016662 oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor(GO:0016662)
0.3 6.0 GO:0016876 aminoacyl-tRNA ligase activity(GO:0004812) ligase activity, forming carbon-oxygen bonds(GO:0016875) ligase activity, forming aminoacyl-tRNA and related compounds(GO:0016876)
0.3 1.8 GO:0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor(GO:0016671)
0.3 9.3 GO:0005506 iron ion binding(GO:0005506)
0.3 2.1 GO:0016833 oxo-acid-lyase activity(GO:0016833)
0.1 1.0 GO:0044822 mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.1 16.4 GO:0042802 identical protein binding(GO:0042802)
0.0 1.2 GO:0043565 sequence-specific DNA binding(GO:0043565)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
2.8 11.2 REACTOME INNATE IMMUNE SYSTEM Genes involved in Innate Immune System
1.2 3.5 REACTOME PURINE METABOLISM Genes involved in Purine metabolism