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GSE55662: Plasticity of transcriptional regulation under antibiotic stress

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Results for Sigma32

Z-value: 2.67

Transcription factors associated with Sigma32

Gene Symbol Gene ID Gene Info
rpoH
rpoH RNA polymerase sigma factor RpoH

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
rpoH0.939.1e-04Click!

Activity profile of Sigma32 motif

Sorted Z-values of Sigma32 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
dnaK-tpke11-dnaJ 14.21
dnaK
dnaJ
tpke11
chaperone protein DnaK
chaperone protein DnaJ
Tpke11
htpG 13.89
htpG
molecular chaperone, HSP90 family
rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF 9.12
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 9.07
rrlC
gltU
rrfC
rrsC
rrlC 23S ribosomal RNA
tRNAgltU
rrfC 5S ribosomal RNA
rrsC 16S ribosomal RNA
groSL 8.66
groS
groL
GroES cochaperonin
GroEL chaperonin
rrsG-gltW-rrlG-rrfG 8.52
rrlG
gltW
rrfG
rrsG
rrlG 23S ribosomal RNA
tRNAgltW
rrfG 5S ribosomal RNA
rrsG 16S ribosomal RNA
raiA 8.20
raiA
stationary phase translation inhibitor and ribosome stability factor
rrsE-gltV-rrlE-rrfE 7.85
rrlE
gltV
rrsE
rrfE
rrlE 23S ribosomal RNA
tRNAgltV
rrsE 16S ribosomal RNA
rrfE 5S ribosomal RNA
bssS 7.75
bssS
regulator of biofilm formation
rrsH-ileV-alaV-rrlH-rrfH 7.54
rrlH
rrfH
rrsH
ileV
alaV
rrlH 23S ribosomal RNA
rrfH 5S ribosomal RNA
rrsH 16S ribosomal RNA
tRNAileV
tRNAalaV
rrsB-gltT-rrlB-rrfB 7.49
rrlB
gltT
rrfB
rrsB
rrlB 23S ribosomal RNA
tRNAgltT
rrfB 5S ribosomal RNA
rrsB 16S ribosomal RNA
rrsA-ileT-alaT-rrlA-rrfA 7.16
rrlA
ileT
alaT
rrsA
rrfA
23S ribosomal RNA (rrlA)
tRNAileT
tRNAalaT
16S ribosomal RNA (rrsA)
5S ribosomal RNA (rrfA)
clpB 7.09
clpB
ClpB chaperone
rpmE 6.83
rpmE
50S ribosomal subunit protein L31
gapA-yeaD 6.52
gapA
yeaD
glyceraldehyde 3-phosphate dehydrogenase
conserved protein
hspQ 6.32
hspQ
heat shock protein, hemimethylated DNA-binding protein
grpE 5.68
grpE
nucleotide exchange factor
clpPX 5.35
clpP
clpX
ClpP
ClpX
ackA 5.31
ackA
acetate kinase
ybbN 5.12
ybbN
chaperone and weak protein oxidoreductase
ldhA 5.04
ldhA
D-lactate dehydrogenase - fermentative
nfuA 4.37
nfuA
iron-sulfur cluster scaffold protein
rlmE-ftsH 4.21
rlmE
ftsH
23S rRNA 2'-O-ribose U2552 methyltransferase
ATP-dependent zinc metalloprotease FtsH
rapA 4.05
rapA
RNA polymerase-binding ATPase and RNAP recycling factor
ibpAB 3.88
ibpA
ibpB
small heat shock protein IbpA
small heat shock protein IbpB
htpX 3.85
htpX
heat shock protein, integral membrane protein
hslVU 3.80
hslV
hslU
peptidase component of the HslVU protease
ATPase component of the HslVU protease
glnS 3.40
glnS
glutamine-tRNA ligase
ybeZYX-lnt 3.35
lnt
ybeZ
ybeX
ybeY
apolipoprotein N-acyltransferase
predicted protein with nucleoside triphosphate hydrolase domain
putative transport protein
endoribonuclease involved in maturation of 16S rRNA and ribosome quality control
ribE-nusB-thiL-pgpA 3.27
nusB
pgpA
ribE
thiL
transcription antitermination protein NusB
phosphatidylglycerophosphatase A
6,7-dimethyl-8-ribityllumazine synthase
thiamine monophosphate kinase
miaA-hfq-hflXKC 3.25
miaA
hflC
hfq
hflK
hflX
tRNA(i6A37) synthase
regulator of FtsH protease
RNA-binding protein that affects many cellular processes; homolog of mammalian Sm/Sm-like proteins
regulator of FtsH protease
ribosome-dissociating factor, GTPase
sdaA 3.00
sdaA
L-serine deaminase I
pncC 2.69
pncC
NMN aminohydrolase
lon 2.60
lon
DNA-binding, ATP-dependent protease La
holC-valS 2.52
valS
holC
valine-tRNA ligase
DNA polymerase III, χ subunit
ppiD 2.48
ppiD
periplasmic folding chaperone
rpoD 2.48
rpoD
RNA polymerase, sigma 70 (sigma D) factor
ybeD-lipB 2.43
ybeD
lipB
conserved protein
lipoyl(octanoyl) transferase
hfq-hflXKC 2.25
hflC
hfq
hflK
hflX
regulator of FtsH protease
RNA-binding protein that affects many cellular processes; homolog of mammalian Sm/Sm-like proteins
regulator of FtsH protease
ribosome-dissociating factor, GTPase
ileS-lspA-fkpB-ispH 2.16
ileS
ispH
fkpB
lspA
isoleucine-tRNA ligase
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
peptidyl-prolyl cis-trans isomerase
prolipoprotein signal peptidase II
mutL-miaA-hfq-hflXKC 2.13
miaA
hflC
hfq
hflK
mutL
hflX
tRNA(i6A37) synthase
regulator of FtsH protease
RNA-binding protein that affects many cellular processes; homolog of mammalian Sm/Sm-like proteins
regulator of FtsH protease
MutL
ribosome-dissociating factor, GTPase
xerD-dsbC-recJ 2.08
recJ
dsbC
xerD
ssDNA-specific exonuclease RecJ
protein disulfide isomerase/protein disulfide oxidoreductase - DsbCreduced
site-specific recombinase
cra 1.89
cra
Cra DNA-binding transcriptional dual regulator
yrfG-hslR 1.56
hslR
yrfG
heat shock protein Hsp15 involved in ribosome recycling
purine nucleotidase
hslRO 1.24
hslR
hslO
heat shock protein Hsp15 involved in ribosome recycling
molecular chaperone Hsp33
lapAB 0.95
lapA
lapB
lipopolysaccharide assembly protein LapA
lipopolysaccharide assembly protein LapB
rnlA 0.88
rnlA
CP4-57 prophage; RNase LS, toxin of the RnlAB toxin-antitoxin system
alaA 0.62
alaA
glutamate-pyruvate aminotransferase
adiC 0.40
adiC
AdiC arginine:agmatine antiporter
ydhQ 0.18
ydhQ
conserved protein

Network of associatons between targets according to the STRING database.

First level regulatory network of Sigma32

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
10.0 30.0 GO:0006986 response to unfolded protein(GO:0006986)
2.6 10.3 GO:0006083 acetate metabolic process(GO:0006083)
2.3 9.1 GO:0043335 protein unfolding(GO:0043335)
2.0 8.2 GO:0045900 negative regulation of translational elongation(GO:0045900)
1.9 7.6 GO:0040033 negative regulation of translation, ncRNA-mediated(GO:0040033) regulation of translation, ncRNA-mediated(GO:0045974) positive regulation of translation, ncRNA-mediated(GO:0045975)
1.5 4.4 GO:0015976 carbon utilization(GO:0015976)
1.3 2.6 GO:0006515 misfolded or incompletely synthesized protein catabolic process(GO:0006515)
1.1 24.9 GO:0006457 protein folding(GO:0006457)
1.1 7.8 GO:0043900 regulation of multi-organism process(GO:0043900) regulation of single-species biofilm formation(GO:1900190)
1.1 3.3 GO:0006772 thiamine metabolic process(GO:0006772) thiamine biosynthetic process(GO:0009228) thiamine-containing compound metabolic process(GO:0042723) thiamine-containing compound biosynthetic process(GO:0042724)
1.0 3.0 GO:0006565 L-serine catabolic process(GO:0006565)
0.8 4.2 GO:0030163 protein catabolic process(GO:0030163)
0.8 2.5 GO:0045903 regulation of translational fidelity(GO:0006450) regulation of DNA-dependent DNA replication initiation(GO:0030174) positive regulation of translational fidelity(GO:0045903)
0.8 3.4 GO:0030490 maturation of SSU-rRNA(GO:0030490)
0.8 3.9 GO:1990169 stress response to copper ion(GO:1990169)
0.5 8.4 GO:0006096 glycolytic process(GO:0006096)
0.4 2.1 GO:0006276 plasmid maintenance(GO:0006276)
0.2 3.4 GO:0043039 tRNA aminoacylation for protein translation(GO:0006418) tRNA aminoacylation(GO:0043039)
0.2 1.6 GO:0034605 cellular response to heat(GO:0034605)
0.2 0.6 GO:0046145 alanine biosynthetic process(GO:0006523) pyruvate family amino acid biosynthetic process(GO:0009079) D-alanine biosynthetic process(GO:0030632) L-alanine biosynthetic process(GO:0042852) D-alanine family amino acid biosynthetic process(GO:0046145) D-amino acid biosynthetic process(GO:0046437)
0.2 2.4 GO:0006633 fatty acid biosynthetic process(GO:0006633)
0.1 0.4 GO:0051454 pH elevation(GO:0045852) intracellular pH elevation(GO:0051454)
0.1 1.9 GO:0006508 proteolysis(GO:0006508)
0.1 0.9 GO:0016071 mRNA catabolic process(GO:0006402) mRNA metabolic process(GO:0016071)
0.0 0.9 GO:0009408 response to heat(GO:0009408)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.9 10.1 GO:0071575 integral component of external side of plasma membrane(GO:0071575)
0.8 2.5 GO:0042575 DNA polymerase complex(GO:0042575)
0.8 23.7 GO:0044445 cytosolic part(GO:0044445)
0.3 2.1 GO:0048476 Holliday junction resolvase complex(GO:0048476)
0.2 91.5 GO:0005829 cytosol(GO:0005829)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
6.0 24.1 GO:0044183 protein binding involved in protein folding(GO:0044183)
2.4 12.2 GO:0004176 ATP-dependent peptidase activity(GO:0004176)
1.9 5.7 GO:0060590 ATPase regulator activity(GO:0060590)
1.8 5.4 GO:0052381 tRNA dimethylallyltransferase activity(GO:0052381)
1.6 6.5 GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity(GO:0004365) glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity(GO:0043891)
1.1 3.4 GO:0016892 endoribonuclease activity, producing 3'-phosphomonoesters(GO:0016892)
1.0 4.1 GO:0001000 bacterial-type RNA polymerase core enzyme binding(GO:0001000)
0.8 2.5 GO:0000996 transcription factor activity, core RNA polymerase binding(GO:0000990) core DNA-dependent RNA polymerase binding promoter specificity activity(GO:0000996) sigma factor activity(GO:0016987)
0.7 2.2 GO:0042380 hydroxymethylbutenyl pyrophosphate reductase activity(GO:0042380)
0.7 7.9 GO:0043024 ribosomal small subunit binding(GO:0043024)
0.7 2.1 GO:0008297 single-stranded DNA exodeoxyribonuclease activity(GO:0008297) 5'-3' exonuclease activity(GO:0008409)
0.7 5.3 GO:0016774 phosphotransferase activity, carboxyl group as acceptor(GO:0016774)
0.6 2.3 GO:0003681 bent DNA binding(GO:0003681)
0.5 3.3 GO:0016776 phosphotransferase activity, phosphate group as acceptor(GO:0016776)
0.5 1.6 GO:0008253 5'-nucleotidase activity(GO:0008253)
0.5 3.0 GO:0016841 ammonia-lyase activity(GO:0016841)
0.5 5.1 GO:0015035 protein disulfide oxidoreductase activity(GO:0015035)
0.4 2.5 GO:0002161 aminoacyl-tRNA editing activity(GO:0002161)
0.4 1.9 GO:0004222 metalloendopeptidase activity(GO:0004222)
0.4 19.2 GO:0016887 ATPase activity(GO:0016887)
0.3 5.0 GO:0051287 NAD binding(GO:0051287)
0.3 3.4 GO:0016875 aminoacyl-tRNA ligase activity(GO:0004812) ligase activity, forming carbon-oxygen bonds(GO:0016875) ligase activity, forming aminoacyl-tRNA and related compounds(GO:0016876)
0.1 0.4 GO:0015181 arginine transmembrane transporter activity(GO:0015181)
0.1 2.3 GO:0051539 4 iron, 4 sulfur cluster binding(GO:0051539)
0.0 0.6 GO:0016769 transaminase activity(GO:0008483) transferase activity, transferring nitrogenous groups(GO:0016769)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.8 2.5 PID CMYB PATHWAY C-MYB transcription factor network

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
1.7 5.0 REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT Genes involved in The citric acid (TCA) cycle and respiratory electron transport