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

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Results for Sigma32

Z-value: 1.29

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
rpoH0.553.2e-03Click!

Activity profile of Sigma32 motif

Sorted Z-values of Sigma32 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
dnaK-tpke11-dnaJ 20.79
dnaK
dnaJ
tpke11
chaperone protein DnaK
chaperone protein DnaJ
Tpke11
htpG 13.29
htpG
molecular chaperone, HSP90 family
groSL 13.10
groS
groL
GroES cochaperonin
GroEL chaperonin
gapA-yeaD 9.35
gapA
yeaD
glyceraldehyde 3-phosphate dehydrogenase
conserved protein
hslVU 7.55
hslV
hslU
peptidase component of the HslVU protease
ATPase component of the HslVU protease
can 6.64
can
carbonic anhydrase 2
ileS-lspA-fkpB-ispH 6.62
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
miaA-hfq-hflXKC 6.34
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
mutL-miaA-hfq-hflXKC 6.27
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
grpE 5.83
grpE
nucleotide exchange factor
rpmE 5.47
rpmE
50S ribosomal subunit protein L31
glnS 5.14
glnS
glutamine-tRNA ligase
hfq-hflXKC 5.01
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
ybfE 4.86
ybfE
LexA-regulated protein
yrdA 4.83
yrdA
conserved protein
ppiD 4.66
ppiD
periplasmic folding chaperone
topA 4.53
topA
DNA topoisomerase I
lapAB-pyrF-yciH 4.30
lapA
pyrF
lapB
yciH
lipopolysaccharide assembly protein LapA
orotidine-5'-phosphate decarboxylase
lipopolysaccharide assembly protein LapB
translation initiation factor
rlmE-ftsH 4.09
rlmE
ftsH
23S rRNA 2'-O-ribose U2552 methyltransferase
ATP-dependent zinc metalloprotease FtsH
holC-valS 4.05
valS
holC
valine-tRNA ligase
DNA polymerase III, χ subunit
ybbN 3.53
ybbN
chaperone and weak protein oxidoreductase
prlC-rsmJ 3.44
rsmJ
prlC
16S rRNA m2G1516 methyltransferase
oligopeptidase A
rdgB-yggW 3.40
yggW
rdgB
predicted oxidoreductase
dITP/XTP pyrophosphatase
clpB 3.31
clpB
ClpB chaperone
hslRO 3.28
hslR
hslO
heat shock protein Hsp15 involved in ribosome recycling
molecular chaperone Hsp33
rfaD-waaFCL 3.25
waaC
waaF
waaL
rfaD
ADP-heptose:LPS heptosyltransferase I
ADP-heptose:LPS heptosyltransferase II
O-antigen ligase
ADP-L-glycero-D-mannoheptose-6-epimerase
lapAB 2.99
lapA
lapB
lipopolysaccharide assembly protein LapA
lipopolysaccharide assembly protein LapB
cra 2.98
cra
Cra DNA-binding transcriptional dual regulator
ribE-nusB-thiL-pgpA 2.81
nusB
pgpA
ribE
thiL
transcription antitermination protein NusB
phosphatidylglycerophosphatase A
6,7-dimethyl-8-ribityllumazine synthase
thiamine monophosphate kinase
ybeZYX-lnt 2.40
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
trmA 2.36
trmA
tRNA m5U54 methyltransferase
yrfG-hslR 2.27
hslR
yrfG
heat shock protein Hsp15 involved in ribosome recycling
purine nucleotidase
phoPQ 2.26
phoQ
phoP
PhoQ sensory histidine kinase
PhoP
clpPX 2.17
clpP
clpX
ClpP
ClpX
yceJI 1.69
yceJ
yceI
predicted cytochrome b561
predicted protein
ydhQ 1.68
ydhQ
conserved protein
slt 1.67
slt
soluble lytic murein transglycosylase
pgpC-tadA 1.54
pgpC
tadA
phosphatidylglycerophosphatase C
tRNA-specific adenosine deaminase
xerD-dsbC-recJ 1.53
recJ
dsbC
xerD
ssDNA-specific exonuclease RecJ
protein disulfide isomerase/protein disulfide oxidoreductase - DsbCreduced
site-specific recombinase
ycjXF-tyrR 1.33
tyrR
ycjX
ycjF
TyrR DNA-binding transcriptional dual regulator
conserved protein
conserved inner membrane protein
htpX 1.08
htpX
heat shock protein, integral membrane protein
ackA 0.99
ackA
acetate kinase
creABC 0.83
creA
creB
creC
conserved protein
CreB transcriptional regulator
CreC
ibpAB 0.69
ibpA
ibpB
small heat shock protein IbpA
small heat shock protein IbpB
ybeD-lipB 0.39
ybeD
lipB
conserved protein
lipoyl(octanoyl) transferase
nfuA 0.12
nfuA
iron-sulfur cluster scaffold 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
12.4 37.2 GO:0006986 response to unfolded protein(GO:0006986)
4.4 17.6 GO:0045974 viral latency(GO:0019042) negative regulation of translation, ncRNA-mediated(GO:0040033) regulation of translation, ncRNA-mediated(GO:0045974) positive regulation of translation, ncRNA-mediated(GO:0045975)
2.4 9.7 GO:0043335 protein unfolding(GO:0043335)
2.2 6.6 GO:0097304 lipoprotein biosynthetic process via signal peptide cleavage(GO:0097304)
1.6 3.3 GO:0042026 protein refolding(GO:0042026)
1.5 4.5 GO:0006265 DNA topological change(GO:0006265)
1.4 4.1 GO:0045903 regulation of translational fidelity(GO:0006450) regulation of DNA-dependent DNA replication initiation(GO:0030174) positive regulation of translational fidelity(GO:0045903)
1.3 21.5 GO:0006457 protein folding(GO:0006457)
1.3 7.5 GO:0031167 rRNA methylation(GO:0031167)
1.1 3.2 GO:0046401 lipopolysaccharide core region biosynthetic process(GO:0009244) lipopolysaccharide core region metabolic process(GO:0046401)
0.9 2.8 GO:0042724 thiamine metabolic process(GO:0006772) thiamine biosynthetic process(GO:0009228) thiamine-containing compound metabolic process(GO:0042723) thiamine-containing compound biosynthetic process(GO:0042724)
0.9 4.3 GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process(GO:0006207) pyrimidine nucleobase biosynthetic process(GO:0019856)
0.8 2.3 GO:0010350 cellular response to magnesium starvation(GO:0010350)
0.7 12.3 GO:0006096 glycolytic process(GO:0006096)
0.6 2.4 GO:0090501 maturation of SSU-rRNA(GO:0030490) RNA phosphodiester bond hydrolysis(GO:0090501)
0.6 2.4 GO:0030488 tRNA methylation(GO:0030488)
0.5 1.5 GO:0002097 tRNA wobble base modification(GO:0002097)
0.4 3.4 GO:1901292 nucleoside phosphate catabolic process(GO:1901292)
0.3 5.1 GO:0043039 tRNA aminoacylation for protein translation(GO:0006418) tRNA aminoacylation(GO:0043039)
0.3 3.0 GO:0008653 lipopolysaccharide metabolic process(GO:0008653)
0.3 2.3 GO:0034605 cellular response to heat(GO:0034605)
0.3 1.5 GO:0006276 plasmid maintenance(GO:0006276)
0.2 1.0 GO:0019541 propionate metabolic process(GO:0019541)
0.2 0.8 GO:0007584 response to nutrient(GO:0007584)
0.2 0.7 GO:1990169 stress response to copper ion(GO:1990169)
0.2 4.8 GO:0051260 protein homooligomerization(GO:0051260)
0.0 0.1 GO:0015976 carbon utilization(GO:0015976)
0.0 0.4 GO:0006633 fatty acid biosynthetic process(GO:0006633)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
2.1 6.3 GO:0032300 mismatch repair complex(GO:0032300)
1.8 16.0 GO:0071575 integral component of external side of plasma membrane(GO:0071575)
1.4 4.1 GO:0042575 DNA polymerase complex(GO:0042575)
0.8 1.5 GO:0048476 Holliday junction resolvase complex(GO:0048476)
0.6 1.7 GO:0009274 peptidoglycan-based cell wall(GO:0009274)
0.5 17.0 GO:0044445 cytosolic part(GO:0044445)
0.3 126.1 GO:0005829 cytosol(GO:0005829)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
9.3 37.2 GO:0044183 protein binding involved in protein folding(GO:0044183)
4.2 12.6 GO:0052381 tRNA dimethylallyltransferase activity(GO:0052381)
2.3 9.4 GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity(GO:0004365) glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity(GO:0043891)
2.2 6.6 GO:0004089 carbonate dehydratase activity(GO:0004089)
2.2 6.6 GO:0042380 hydroxymethylbutenyl pyrophosphate reductase activity(GO:0042380)
1.9 5.8 GO:0060590 ATPase regulator activity(GO:0060590)
1.5 4.5 GO:0003916 DNA topoisomerase activity(GO:0003916)
1.4 8.6 GO:0004222 metalloendopeptidase activity(GO:0004222)
1.3 5.0 GO:0003681 bent DNA binding(GO:0003681)
1.1 3.4 GO:0004551 nucleotide diphosphatase activity(GO:0004551)
1.1 4.4 GO:0008962 phosphatidylglycerophosphatase activity(GO:0008962)
1.1 2.2 GO:0004176 ATP-dependent peptidase activity(GO:0004176)
0.8 2.3 GO:0008253 5'-nucleotidase activity(GO:0008253)
0.7 4.1 GO:0002161 aminoacyl-tRNA editing activity(GO:0002161)
0.6 2.4 GO:0008175 tRNA binding(GO:0000049) tRNA methyltransferase activity(GO:0008175)
0.5 1.5 GO:0008297 single-stranded DNA exodeoxyribonuclease activity(GO:0008297) 5'-3' exonuclease activity(GO:0008409)
0.5 5.1 GO:0004812 aminoacyl-tRNA ligase activity(GO:0004812) ligase activity, forming carbon-oxygen bonds(GO:0016875) ligase activity, forming aminoacyl-tRNA and related compounds(GO:0016876)
0.4 5.2 GO:0004175 endopeptidase activity(GO:0004175)
0.4 2.4 GO:0016894 endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters(GO:0016894)
0.4 3.5 GO:0015035 protein disulfide oxidoreductase activity(GO:0015035)
0.4 3.2 GO:0050661 NADP binding(GO:0050661)
0.3 15.4 GO:0042623 ATPase activity, coupled(GO:0042623)
0.3 2.7 GO:0043024 ribosomal small subunit binding(GO:0043024)
0.2 3.1 GO:0000155 phosphorelay sensor kinase activity(GO:0000155) protein histidine kinase activity(GO:0004673)
0.1 1.0 GO:0016774 phosphotransferase activity, carboxyl group as acceptor(GO:0016774)
0.1 4.5 GO:0008270 zinc ion binding(GO:0008270)
0.1 1.7 GO:0016757 transferase activity, transferring glycosyl groups(GO:0016757)
0.0 3.0 GO:0046872 metal ion binding(GO:0046872)
0.0 4.7 GO:0042802 identical protein binding(GO:0042802)
0.0 1.3 GO:0005524 ATP binding(GO:0005524)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
1.6 4.7 PID CMYB PATHWAY C-MYB transcription factor network