Rv0117 (oxyS)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: oxidative stress response regulatory protein oxyS
- REFSEQ: oxidative stress response regulatory protein OXYS
- PATRIC: Hydrogen peroxide-inducible genes activator
- TUBERCULIST: Oxidative stress response regulatory protein OxyS
- NCBI: Oxidative stress response regulatory protein OxyS
- updated information (H37Rv4):
  - gene name: oxyS
  - function:
  - reference:
Type: Not Target
Start: 141200
End: 142144
Operon:

Trans-membrane region:
Role: I.J.1 - Repressors/activators
GO terms:
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0003700 - DNA binding transcription factor activity (Uniprot)
- GO:0003677 - DNA binding (Uniprot)
- GO:0000986 - bacterial-type proximal promoter sequence-specific DNA binding (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure:
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
5XXP	42%	Cupriavidus necator	Crystal structure of CbnR_DBD-DNA complex
2H98	37%	Acinetobacter sp.	Crystal structure of the effector binding domain of a CatM variant, CatM(V158M)
4IHT	36%	Acinetobacter sp.	Crystal Structure of BenM_DBD/benA site 1 DNA Complex
4IHS	36%	Acinetobacter sp.	Crystal Structure of BenM_DBD/catB site 1 DNA Complex
3M1E	36%	Acinetobacter sp. ADP1	Crystal Structure of BenM_DBD

Links to additional information on oxyS:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -0.046 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VLFRQLEYFVAVAQERHFARAAEKCYVSQPALSSAIAKLERELNVTLINRGHSFEGLTREGERLVVWAKRILAEHAAFKAEVDAVRSGITGTLRLGTVPT
ASTTASLVLSAFCSAHPLAKVQVCSRLAATELYRRLREFELDAVIVHPETQDSDDVDLVPLYEEQYVLLSPADMLPPGTSTLVWRDAAQLPLALLTADMR
DRQVIDAAFADHAVSAIPQVETDSVASLFAQVATGNWASIVPHTWLWAMPMSGPTGGEIRAVELVDPVLKAQIALATNALGPGSPVARALITCAQALALN
EFFDTQLRGITRRR

(Nucleotide sequence available on KEGG)

Additional Information

Analysis of Positive Selection in Clinical Isolates new

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.38 (0.21)	1.55 (0.82)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv0117/oxyS, gene len: 944 bp, num TA sites: 17

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	non-essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	non-essential	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	non-essential	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	non-essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	non-essential	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=-0.55)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	non-essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	non-essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=-0.337)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	non-essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	non-essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, vitamins)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=0.14)	YM rich vs minimal medium	resampling

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

Binds To:
Bound By:

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- Rv0167 (yrbE1A) (Direct binding)
- Rv1795 (eccD5) (Direct binding)
- Rv0168 (yrbE1B) (Upstream of operon)
- Rv0169 (mce1A) (Upstream of operon)
- Rv0170 (mce1B) (Upstream of operon)
- Rv0171 (mce1C) (Upstream of operon)
- Rv0172 (mce1D) (Upstream of operon)
- Rv0173 (lprK) (Upstream of operon)
- Rv0174 (mce1F) (Upstream of operon)
- Rv0175 (-) (Upstream of operon)
- Rv0176 (-) (Upstream of operon)
- Rv0177 (-) (Upstream of operon)
- Rv0178 (-) (Upstream of operon)
- Rv1796 (mycP5) (Upstream of operon)
- Rv1797 (eccE5) (Upstream of operon)
- Rv1798 (eccA5) (Upstream of operon)
Bound By:
- Rv0967 (csoR) (Direct binding)
- Rv1816 (-) (Direct binding)
- Rv3133c (devR) (Direct binding)

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
Upregulated by:
Downregulates:
- Rv0118c (oxcA)
- Rv0119 (fadD7)
Downregulated by:
- Rv0576 (-)

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv0117 (oxyS)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv2939	ashwinigbhat	IDA		One hybrid System DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005
Interaction	Regulatory Rv2939	ashwinigbhat	IDA		One hybrid System M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv2935	ashwinigbhat	IDA		One hybrid System M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv2935	ashwinigbhat	IDA		One hybrid System DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005
Interaction	Regulatory Rv2934	ashwinigbhat	IDA		One hybrid System DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005
Interaction	Regulatory Rv2934	ashwinigbhat	IDA		One hybrid System M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv2933	ashwinigbhat	IDA		One hybrid System M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv2933	ashwinigbhat	IDA		One hybrid System DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005
Interaction	Regulatory Rv2932	ashwinigbhat	IDA		One hybrid System DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005
Interaction	Regulatory Rv2932	ashwinigbhat	IDA		One hybrid System M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv2931	ashwinigbhat	IDA		One hybrid System M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv2931	ashwinigbhat	IDA		One hybrid System DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005
Interaction	Regulatory Rv2930	ashwinigbhat	IDA		One hybrid System DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005
Interaction	Regulatory Rv2930	ashwinigbhat	IDA		One hybrid System M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv1911c	shahanup86	IEP		Co-expression (Functional linkage) M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv1912c	shahanup86	IEP		Co-expression (Functional linkage) M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	shahanup86	IEP	19228590	Co-expression (Functional linkage)
Interaction	Regulatory Rv1907c	shahanup86	IEP		Co-expression (Functional linkage) M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv1908c	shahanup86	IEP		Co-expression (Functional linkage) M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv1909c	shahanup86	IEP		Co-expression (Functional linkage) M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	Regulatory Rv1910c	shahanup86	IEP		Co-expression (Functional linkage) M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv0182c	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. JH. Lee, DE. Geiman et al. Role of stress response sigma factor SigG in Mycobacterium tuberculosis. J. Bacteriol. 2008
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2938	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2939	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3537	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3538	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2934	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2935	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2936	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2937	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2930	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2931	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2932	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv2933	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1909c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1910c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1911c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1912c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1907c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1908c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	ISO	18985025	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv2428	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	ISO	18985025	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv3913	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	ISO	18985025	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv0117	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv0117	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	ISO	18985025	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv1908c	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	Regulates Rv3913	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
Citation	Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006	yamir.moreno	ISO	16530225	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv0117	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
Interaction	RegulatedBy Rv0117	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
Citation	Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006	yamir.moreno	ISO	16530225	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv1908c	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
Citation	Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006	yamir.moreno	ISO	16530225	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv2428	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
Citation	Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006	yamir.moreno	ISO	16530225	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.

Property

Value

Creator

Evidence

PMID

Comment

Interaction

Regulatory Rv2939

ashwinigbhat

IDA

One hybrid System
DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005

Interaction

Regulatory Rv2939

ashwinigbhat

IDA

One hybrid System
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv2935

ashwinigbhat

IDA

One hybrid System
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv2935

ashwinigbhat

IDA

One hybrid System
DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005

Interaction

Regulatory Rv2934

ashwinigbhat

IDA

One hybrid System
DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005

Interaction

Regulatory Rv2934

ashwinigbhat

IDA

One hybrid System
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv2933

ashwinigbhat

IDA

One hybrid System
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv2933

ashwinigbhat

IDA

One hybrid System
DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005

Interaction

Regulatory Rv2932

ashwinigbhat

IDA

One hybrid System
DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005

Interaction

Regulatory Rv2932

ashwinigbhat

IDA

One hybrid System
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv2931

ashwinigbhat

IDA

One hybrid System
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv2931

ashwinigbhat

IDA

One hybrid System
DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005

Interaction

Regulatory Rv2930

ashwinigbhat

IDA

One hybrid System
DM. Collins, B. Skou et al. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect. Immun. 2005

Interaction

Regulatory Rv2930

ashwinigbhat

IDA

One hybrid System
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv1911c

shahanup86

IEP

Co-expression (Functional linkage)
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv1912c

shahanup86

IEP

Co-expression (Functional linkage)
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

shahanup86

IEP

19228590

Co-expression (Functional linkage)

Interaction

Regulatory Rv1907c

shahanup86

IEP

Co-expression (Functional linkage)
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv1908c

shahanup86

IEP

Co-expression (Functional linkage)
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv1909c

shahanup86

IEP

Co-expression (Functional linkage)
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

Regulatory Rv1910c

shahanup86

IEP

Co-expression (Functional linkage)
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Interaction

RegulatedBy Rv0182c

yamir.moreno

IEP

Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments..
JH. Lee, DE. Geiman et al. Role of stress response sigma factor SigG in Mycobacterium tuberculosis. J. Bacteriol. 2008

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2938

yamir.moreno

IDA

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2939

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv3537

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv3538

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2934

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2935

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2936

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2937

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2930

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2931

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2932

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv2933

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv1909c

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv1910c

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv1911c

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv1912c

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv1907c

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv1908c

yamir.moreno

IDA

Citation

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008

yamir.moreno

ISO

18985025

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.

Interaction

Regulates Rv2428

yamir.moreno

ISO

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008

Citation

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008

yamir.moreno

ISO

18985025

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.

Interaction

Regulates Rv3913

yamir.moreno

ISO

Citation

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008

yamir.moreno

ISO

18985025

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.

Interaction

Regulates Rv0117

yamir.moreno

ISO

Interaction

RegulatedBy Rv0117

yamir.moreno

ISO

Citation

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008

yamir.moreno

ISO

18985025

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.

Interaction

Regulates Rv1908c

yamir.moreno

ISO

Interaction

Regulates Rv3913

yamir.moreno

ISO

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006

Citation

Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006

yamir.moreno

ISO

16530225

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.

Interaction

Regulates Rv0117

yamir.moreno

ISO

Interaction

RegulatedBy Rv0117

yamir.moreno

ISO

Citation

Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006

yamir.moreno

ISO

16530225

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.

Interaction

Regulates Rv1908c

yamir.moreno

ISO

Citation

Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006

yamir.moreno

ISO

16530225

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.

Interaction

Regulates Rv2428

yamir.moreno

ISO

Citation

Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006

yamir.moreno

ISO

16530225

E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.

Comments

TB Genome Annotation Portal

Rv0117 (oxyS)

Amino Acid Sequence

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

Interactions based on ChIPSeq data

Interactions based on ChIPSeq data (Minch et al. 2014)

Interactions based on TFOE data (Rustad et al. 2014)

TBCAP

Comments

Analysis of Positive Selection in Clinical Isolates new