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

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Results for SoxS

Z-value: 1.12

Transcription factors associated with SoxS

Gene Symbol Gene ID Gene Info
soxS
soxS SoxS DNA-binding transcriptional dual regulator

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
soxS0.756.6e-06Click!

Activity profile of SoxS motif

Sorted Z-values of SoxS motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
tolC-ygiABC 16.93
ygiC
ygiB
ygiA
tolC
predicted enzyme with ATPase activity
conserved outer membrane protein
predicted protein
TolC outer membrane channel
ptsG 12.00
ptsG
glucose PTS permease - PtsG subunit
sodA 11.77
sodA
superoxide dismutase (Mn)
fldA-uof-fur 11.74
fur
uof
fldA
Fur transcriptional dual regulator
RyhB-regulated fur leader peptide
flavodoxin 1
acrAB 8.04
acrB
acrA
AcrAB-TolC multidrug efflux pump - permease subunit
AcrAB-TolC multidrug efflux pump - membrane fusion protein
ybjC-nfsA-rimK-ybjN 7.13
nfsA
ybjN
ybjC
rimK
NADPH nitroreductase NfsA
predicted oxidoreductase
predicted inner membrane protein
ribosomal protein S6 modification protein
pgi 6.38
pgi
phosphoglucose isomerase
uof-fur 4.56
fur
uof
Fur transcriptional dual regulator
RyhB-regulated fur leader peptide
zwf 4.24
zwf
glucose-6-phosphate dehydrogenase (NADP+)
acrZ 3.29
acrZ
small membrane protein that interacts with the AcrAB-TolC multidrug efflux pump
soxS 3.04
soxS
SoxS DNA-binding transcriptional dual regulator
ydbK-ompN 2.93
ydbK
ompN
pyruvate:flavodoxin oxidoreductase
outer membrane pore protein N, non-specific
nfsB 2.58
nfsB
NAD(P)H nitroreductase NfsB
ydbK 1.35
ydbK
pyruvate:flavodoxin oxidoreductase
pqiAB 1.24
pqiB
pqiA
paraquat-inducible protein B
paraquat-inducible protein A
nfo 1.00
nfo
endonuclease IV
ribA 0.68
ribA
GTP cyclohydrolase II
inaA 0.29
inaA
pH-inducible protein involved in stress response

Network of associatons between targets according to the STRING database.

First level regulatory network of SoxS

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
3.9 11.8 GO:0006801 superoxide metabolic process(GO:0006801)
3.0 12.0 GO:0046323 glucose transport(GO:0015758) glucose import(GO:0046323)
2.8 16.9 GO:0015891 siderophore transport(GO:0015891)
2.4 7.1 GO:1902209 negative regulation of organelle organization(GO:0010639) negative regulation of cell projection organization(GO:0031345) post-translational protein modification(GO:0043687) response to alcohol(GO:0097305) regulation of single-species biofilm formation on inanimate substrate(GO:1900231) negative regulation of single-species biofilm formation on inanimate substrate(GO:1900232) negative regulation of organelle assembly(GO:1902116) negative regulation of bacterial-type flagellum assembly(GO:1902209)
1.4 4.2 GO:0009372 quorum sensing(GO:0009372)
1.1 3.3 GO:0036460 cellular response to cell envelope stress(GO:0036460)
0.9 8.0 GO:0006855 drug transmembrane transport(GO:0006855)
0.9 2.6 GO:0046263 trinitrotoluene metabolic process(GO:0018973) 2,4,6-trinitrotoluene metabolic process(GO:0018974) nitrotoluene metabolic process(GO:0019326) 2,4,6-trinitrotoluene catabolic process(GO:0046256) trinitrotoluene catabolic process(GO:0046260) nitrotoluene catabolic process(GO:0046263) toluene-containing compound metabolic process(GO:0072490) toluene-containing compound catabolic process(GO:0072491)
0.5 6.4 GO:0034599 cellular response to oxidative stress(GO:0034599)
0.5 16.3 GO:0006417 regulation of translation(GO:0006417)
0.3 2.9 GO:0034219 carbohydrate transmembrane transport(GO:0034219)
0.2 1.0 GO:0006284 base-excision repair(GO:0006284)
0.2 0.7 GO:0009231 riboflavin metabolic process(GO:0006771) riboflavin biosynthetic process(GO:0009231) flavin-containing compound metabolic process(GO:0042726) flavin-containing compound biosynthetic process(GO:0042727)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.5 25.0 GO:1990351 transmembrane transporter complex(GO:1902495) transporter complex(GO:1990351)
0.1 45.5 GO:0005829 cytosol(GO:0005829)
0.1 3.3 GO:0009279 cell outer membrane(GO:0009279)
0.0 4.2 GO:0016020 membrane(GO:0016020)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
3.9 11.8 GO:0016721 superoxide dismutase activity(GO:0004784) oxidoreductase activity, acting on superoxide radicals as acceptor(GO:0016721)
2.8 16.9 GO:0015562 efflux transmembrane transporter activity(GO:0015562)
2.7 8.0 GO:0015307 drug:proton antiporter activity(GO:0015307)
2.4 7.1 GO:0034567 chromate reductase activity(GO:0034567)
1.0 3.0 GO:0001098 basal transcription machinery binding(GO:0001098) bacterial-type RNA polymerase holo enzyme binding(GO:0001108)
0.8 12.0 GO:0090563 protein-phosphocysteine-sugar phosphotransferase activity(GO:0090563)
0.4 6.4 GO:0016861 intramolecular oxidoreductase activity, interconverting aldoses and ketoses(GO:0016861)
0.3 3.3 GO:0015238 drug transmembrane transporter activity(GO:0015238)
0.3 2.6 GO:0016646 oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor(GO:0016646)
0.3 2.9 GO:0015288 porin activity(GO:0015288) wide pore channel activity(GO:0022829)
0.2 0.7 GO:0019238 cyclohydrolase activity(GO:0019238)
0.1 4.2 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor(GO:0016616)
0.1 1.0 GO:0004520 endodeoxyribonuclease activity(GO:0004520)
0.1 6.9 GO:0008270 zinc ion binding(GO:0008270)