Rv0117 Hydrogen peroxide-inducible genes activator

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0117 oxyS Hydrogen peroxide-inducible genes activator CDS 141200 142144 + 945 314 TRUE

Rv0117 (Hydrogen peroxide-inducible genes activator) is predicted to be co-regulated in modules bicluster_0260 with residual 0.50 and bicluster_0311 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.86 for bicluster_0260 and 0.00 and 0.00 for bicluster_0311 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 2 of 2
Gene Target Differential Expression Distance Expression pvalue Type
No -120 0.28 0.972539 Primary.TSS
Type VII secretion integral membrane protein EccD
No -64 0.11 0.927661 Primary.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Two component transcriptional regulatory protein DevR
No -124 -0.21 0.297718 Primary.TSS
No -53 -0.19 0.999609 Primary.TSS
Transcriptional regulator, TetR family
No 43 0.16 0.882886 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0260
e.value: 
0.00000000083
Motif Bicluster: 
e.value: 
0.86
Motif Bicluster: 
0.50
bicluster_0311
e.value: 
0.0000094
Motif Bicluster: 
e.value: 
0.00031
Motif Bicluster: 
0.51
Product (LegacyBRC) Product (RefSeq)
OXIDATIVE STRESS RESPONSE REGULATORY PROTEIN OXYS oxidative stress response regulatory protein OXYS
Operon # Operon
78
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

not assigned to any KEGG Pathway.
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607259 NP_214631.1 Run
Description:Expression data from transcription factor over expression experiments. TFOE are matched to the ChIP-seq experiment done simultaneously. This dataset is described in Rustad et al. 2014, Genome Biology.
BioProject Accession GEO Series References Repository Sample Method Sample Type
PRJNA254351 GSM1426406 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426407 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426408 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426409 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0117_B257 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.490000 1.00

How essentiality calculations were done?

The relative representation of each mutant was determined by calculating the fold change (sequence reads/insertion in cholesterol divided by sequence reads/insertion in glycerol) for each gene. Statistical significance was determined by t-test. Each insertion site in each replicate sample was treated as a separate data point. The hyperbola used for defining genes specifically required for growth in cholesterol was defined by the formula, y = 3.8/x+0.7. Genes above this line are annotated as required for growth on cholesterol.

TRIP log2 fold abundance change

reports the log2 abundance fold change of each TFI strain, relative to no induction, in absence or presence of drug, averaged across experimental replicates. Also reported are the accompanying z-scores and two-sided t-test p-values for each TFI strain under each condition. Please refer to Ma et al., 2020, Nature Microbiology for more information.

p-value Untreated: 0.31313
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 9.00 U
D3I 3 3 3.83 7.79 I
D3U 3 3 3.83 7.51 U
D5I 9 5 6.00 11.47 I
D5U 17 5 6.00 11.69 U
D7I 18 7 8.14 8.93 I
D7U 19 7 8.14 9.11 U
D14I 4 14 15.63 5.69 I
D14U 4 14 15.63 7.47 U
D17I 3 17 19.15 4.62 I
D17U 3 17 19.15 7.63 U
D21I 4 21 23.23 4.69 I
D21U 4 21 23.23 7.66 U
D24I 3 24 26.60 1.96 I
D24U 3 24 26.60 7.54 U
D28I 4 28 30.61 3.76 I
D28U 4 28 30.61 8.13 U